5WXV | pdb_00005wxv

The crystal structure of VabB-ICL domain from Vibrio anguillarum 775

PDB DOI: https://doi.org/10.2210/pdb5WXV/pdb

Classification: LYASE
Organism(s): Vibrio anguillarum 775
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-01-09 Released: 2018-01-17
Deposition Author(s): Du, J., Ma, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.273 (Depositor), 0.270 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The crystal structures of isochorismatase domains from Vibrio anguillarum 775

Du, J., Ma, Q.

To be published.

Macromolecule Content

Total Structure Weight: 295.85 kDa
Atom Count: 19,230
Modeled Residue Count: 2,376
Deposited Residue Count: 2,604
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isochorismate lyase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	217	Vibrio anguillarum 775	Mutation(s): 0 Gene Names: vabB EC: 3.3.2.1
UniProt
Find proteins for Q5DK16 (Vibrio anguillarum (strain ATCC 68554 / 775)) Explore Q5DK16 Go to UniProtKB: Q5DK16
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5DK16
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.273 (Depositor), 0.270 (DCC)
R-Value Work: 0.206 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.527	α = 90
b = 173.882	β = 90
c = 143.764	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-01-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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.