5HWG

Structure of a cysteine hydrolase with a negative substrate

PDB DOI: https://doi.org/10.2210/pdb5HWG/pdb

Classification: HYDROLASE
Organism(s): Microbacterium hydrocarbonoxydans
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-01-29 Released: 2017-02-01
Deposition Author(s): Feng, Y., Gao, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.237
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

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

Literature

Structure of a cysteine hydrolase

Gao, S., Feng, Y.

To be published.

Macromolecule Content

Total Structure Weight: 20.53 kDa
Atom Count: 1,458
Modelled Residue Count: 175
Deposited Residue Count: 187
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isochorismatase	A	187	Microbacterium hydrocarbonoxydans	Mutation(s): 1
UniProt
Find proteins for A0A0K0XHU0 (Microbacterium hydrocarbonoxydans) Explore A0A0K0XHU0 Go to UniProtKB: A0A0K0XHU0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0K0XHU0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
66Y Query on 66Y Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(1S,4R)-2-azabicyclo[2.2.1]hept-5-en-3-one C₆ H₇ N O DDUFYKNOXPZZIW-CRCLSJGQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.237
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.291	α = 90
b = 69.291	β = 90
c = 86.617	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2019-02-20
Changes: Data collection, Source and taxonomy
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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.