5HWH | pdb_00005hwh

Structure of a cysteine hydrolase with a positive substrate

PDB DOI: https://doi.org/10.2210/pdb5HWH/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: 1.79 Å
R-Value Free:
0.220 (Depositor), 0.206 (DCC)
R-Value Work:
0.184 (Depositor), 0.173 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5HWH

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: 1,583
Modeled Residue Count: 175
Deposited Residue Count: 187
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0K0XHU0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
66Z Query on 66Z 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]	(1~{S},4~{R})-3-azabicyclo[2.2.1]hept-5-en-2-one C₆ H₇ N O DDUFYKNOXPZZIW-UHNVWZDZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.220 (Depositor), 0.206 (DCC)
R-Value Work: 0.184 (Depositor), 0.173 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.427	α = 90
b = 69.427	β = 90
c = 87.159	γ = 120

Software Package:

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

Structure Validation

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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

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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.