3KWO | pdb_00003kwo

Crystal Structure of Putative Bacterioferritin from Campylobacter jejuni

PDB DOI: https://doi.org/10.2210/pdb3KWO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-12-01 Released: 2010-01-19
Deposition Author(s): Kim, Y., Gu, M., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.197 (Depositor), 0.195 (DCC)
R-Value Work:
0.144 (Depositor), 0.142 (DCC)
R-Value Observed:
0.146 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Putative Bacterioferritin from Campylobacter jejuni

Kim, Y., Gu, M., Papazisi, L., Anderson, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 74.72 kDa
Atom Count: 5,550
Modelled Residue Count: 591
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative bacterioferritin	A, B, C, D	152	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0 EC: 1.16
UniProt
Find proteins for Q0P891 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P891 Go to UniProtKB: Q0P891
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0P891
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain N [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain N [auth A]	AA [auth B], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain N [auth A] Interactions & Density Focus chain AA [auth B] Focus chain N [auth A]
BU1 Query on BU1 Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain ZA [auth D]	AB [auth D], BA [auth B], ZA [auth D]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain BA [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth B] Focus chain ZA [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain P [auth A] SDF format, chain RA [auth C] SDF format, chain T [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain T [auth A] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain P [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain T [auth A]	BB [auth D] CA [auth B] CB [auth D] DA [auth B] DB [auth D] BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], IA [auth B], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], T [auth A], U [auth A], V [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], SA [auth D], TA [auth D], UA [auth D], VA [auth D], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.197 (Depositor), 0.195 (DCC)
R-Value Work: 0.144 (Depositor), 0.142 (DCC)
R-Value Observed: 0.146 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33kwo

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.715	α = 90
b = 91.715	β = 90
c = 202.288	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary