5KVB | pdb_00005kvb

The crystal structure of hexachlorocyclohexane dehydrochlorinase LinA-type3 from Novosphingobium barchaimii LL02

PDB DOI: https://doi.org/10.2210/pdb5KVB/pdb

Classification: LYASE
Organism(s): Novosphingobium barchaimii LL02
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-07-14 Released: 2017-07-19
Deposition Author(s): Dellas, N., Oakeshott, J., Pearce, S.L., Pandey, G., Pushiri, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.200 (Depositor), 0.201 (DCC)
R-Value Work:
0.164 (Depositor), 0.166 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5KVB

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

Literature

The crystal structure of hexachlorocyclohexane dehydrochlorinase LinA-type3 from Novosphingobium barchaimii LL02

Dellas, N., Oakeshott, J., Pearce, S.L., Pandey, G., Pushiri, H.

To be published.

Macromolecule Content

Total Structure Weight: 17.72 kDa
Atom Count: 1,339
Modeled Residue Count: 146
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-hexachlorocyclohexane dehydrochlorinase	A	156	Novosphingobium barchaimii LL02	Mutation(s): 0 Gene Names: V474_07160
UniProt
Find proteins for A0A0J7XEF9 (Novosphingobium barchaimii LL02) Explore A0A0J7XEF9 Go to UniProtKB: A0A0J7XEF9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0J7XEF9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.200 (Depositor), 0.201 (DCC)
R-Value Work: 0.164 (Depositor), 0.166 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.169	α = 90
b = 50.169	β = 90
c = 147.968	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-07-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-19
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.