6KW6

Crystal Structure of cytidine deaminase from Streptomyces noursei

PDB DOI: https://doi.org/10.2210/pdb6KW6/pdb

Classification: HYDROLASE
Organism(s): Streptomyces noursei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-06 Released: 2020-09-09
Deposition Author(s): Xie, T., Liu, Z.C., Wang, G.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.192
R-Value Work: 0.168
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of cytidine deaminase from Streptomyces noursei

Xie, T., Liu, Z.C., Wang, G.G.

To be published.

Macromolecule Content

Total Structure Weight: 28.09 kDa
Atom Count: 1,864
Modelled Residue Count: 238
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytidine deaminase	A, B	135	Streptomyces noursei	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-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: 1.90 Å
R-Value Free: 0.192
R-Value Work: 0.168
R-Value Observed: 0.169
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.773	α = 90
b = 74.259	β = 106.57
c = 52.785	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-09-09
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 R01GM133198.