5ZTD | pdb_00005ztd

X-ray Crystal Structure of Pseudoazurin Met16Val Variant

PDB DOI: https://doi.org/10.2210/pdb5ZTD/pdb

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

Deposited: 2018-05-02 Released: 2019-05-15
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: 1.05 Å
R-Value Free:
0.151 (Depositor), 0.150 (DCC)
R-Value Work:
0.114 (Depositor), 0.120 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

X-ray Crystal Structure of Pseudoazurin Met16Val Variant

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

To be published.

Macromolecule Content

Total Structure Weight: 26.13 kDa
Atom Count: 2,647
Modeled Residue Count: 248
Deposited Residue Count: 248
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, B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19567
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.151 (Depositor), 0.150 (DCC)
R-Value Work: 0.114 (Depositor), 0.120 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.07	α = 90
b = 60.56	β = 106.2
c = 54.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SHELXL	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-05-15

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: 2019-05-15
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.