5YW3 | pdb_00005yw3

X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant

PDB DOI: https://doi.org/10.2210/pdb5YW3/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Achromobacter cycloclastes
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-11-28 Released: 2018-11-28
Deposition Author(s): Sakai, C., Yamaguchi, T., Kohzuma, T.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.173 (Depositor), 0.178 (DCC)
R-Value Work:
0.127 (Depositor), 0.132 (DCC)
R-Value Observed:
0.129 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

X-ray Crystal Structure of Pseudoazurin Thr36Lys Variant

Yamaguchi, T., Sakai, C., Kohzuma, T.

To be published.

Macromolecule Content

Total Structure Weight: 52.6 kDa
Atom Count: 4,913
Modeled Residue Count: 496
Deposited Residue Count: 496
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudoazurin	A, B, C, D	124	Achromobacter cycloclastes	Mutation(s): 1 Gene Names: bcp
UniProt
Find proteins for P19567 (Achromobacter cycloclastes) Explore P19567 Go to UniProtKB: P19567
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19567
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain H [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], H [auth C], J [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain J [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	G [auth B], I [auth C], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free: 0.173 (Depositor), 0.178 (DCC)
R-Value Work: 0.127 (Depositor), 0.132 (DCC)
R-Value Observed: 0.129 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.699	α = 88.88
b = 51.227	β = 77.16
c = 57.723	γ = 86.58

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	22550145

Revision History (Full details and data files)

Version 1.0: 2018-11-28
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.