6O49

CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF339

PDB DOI: https://doi.org/10.2210/pdb6O49/pdb

Classification: ISOMERASE, PROTEIN BINDING
Organism(s): Saccharomyces cerevisiae S288C, Burkholderia pseudomallei 1710b
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-02-28 Released: 2020-02-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.211
R-Value Work: 0.168
R-Value Observed: 0.171

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF339

Iwasaki, J., Lorimer, D.D., Vivoli, M., Harmer, N.J., Kibble, E.A., Peacock, C.S., Abendroth, J., Mayclin, S.J., Dranow, D.M., Pierce, P.G., Fox III, D., Lewis, M., Bzdyl, N., Kristensen, S., Schmidberger, J.W., Bond, C.B., Seufert, F., Schmitz, J., Norville, I.H., Myler, P.J., Holzgrabe, U., Sarkar-Tyson, M.

To be published.

Macromolecule Content

Total Structure Weight: 47.31 kDa
Atom Count: 3,374
Modelled Residue Count: 380
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase	A, B	209	Saccharomyces cerevisiae S288C, Burkholderia pseudomallei 1710b This entity is chimeric	Mutation(s): 0 Gene Names: SMT3, YDR510W, D9719.15, BURPS1710b_A0907 EC: 5.2.1.8
UniProt
Find proteins for Q3JK38 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JK38 Go to UniProtKB: Q3JK38
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306 Go to UniProtKB: Q12306
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q3JK38Q12306
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LL7 Query on LL7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(2~{S})-~{N}-[3-oxidanylidene-3-[(3,4,5-trimethoxyphenyl)amino]propyl]-1-(phenylmethyl)sulfonyl-piperidine-2-carboxamide C₂₅ H₃₃ N₃ O₇ S WNVXSKRDYHCOMK-FQEVSTJZSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	E [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.211
R-Value Work: 0.168
R-Value Observed: 0.171
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m36o49

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.86	α = 90
b = 33.6	β = 101.21
c = 98.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-02-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-02-12
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-04-03
Changes: Refinement description

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Deposit Data

Help and Resources

6O49

CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF339

CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF339

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)