4YL4 | pdb_00004yl4

1.1 Angstrom resolution X-ray Crystallographic Structure of Psudoazurin

PDB DOI: https://doi.org/10.2210/pdb4YL4/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Achromobacter cycloclastes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-03-05 Released: 2016-03-09
Deposition Author(s): Yamaguchi, T., Asamura, S., Takashina, A., Unno, M., Kohzuma, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.186 (Depositor), 0.180 (DCC)
R-Value Work:
0.148 (Depositor), 0.150 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling

Yamaguchi, T., Akao, K., Takashina, A., Asamura, S., Unno, M., Szilagyi, R.K., Kohzuma, T.

(2016) RSC Adv 6: 88358-88365

DOI: https://doi.org/10.1039/C6RA19282C

Macromolecule Content

Total Structure Weight: 13.37 kDa
Atom Count: 1,214
Modelled Residue Count: 124
Deposited Residue Count: 124
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudoazurin	A	124	Achromobacter cycloclastes	Mutation(s): 0 Gene Names: bcp
UniProt
Find proteins for P19567 (Achromobacter cycloclastes) Explore P19567 Go to UniProtKB: P19567
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19567
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.186 (Depositor), 0.180 (DCC)
R-Value Work: 0.148 (Depositor), 0.150 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.019	α = 90
b = 63.2	β = 90
c = 67.045	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2016-12-28
Changes: Database references
Version 1.2: 2020-01-29
Changes: Data collection, Derived calculations
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description

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1.1 Angstrom resolution X-ray Crystallographic Structure of Psudoazurin

X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

4YL4 | pdb_00004yl4