2BCO | pdb_00002bco

X-ray structure of succinylglutamate desuccinalase from Vibrio Parahaemolyticus (RIMD 2210633) at the resolution 2.3 A, Northeast Structural Genomics Target Vpr14

PDB DOI: https://doi.org/10.2210/pdb2BCO/pdb

Classification: HYDROLASE
Organism(s): Vibrio parahaemolyticus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-10-19 Released: 2005-10-25
Deposition Author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Benach, J., Zhou, W., Acton, T., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.267 (Depositor), 0.280 (DCC)
R-Value Work:
0.213 (Depositor), 0.225 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2BCO

This is version 1.3 of the entry. See complete history.

Literature

X-ray structure of succinylglutamate desuccinalase from Vibrio Parahaemolyticus (RIMD 2210633) at the resolution 2.3 A, Northeast Structural Genomics Target Vpr14

Kuzin, A.P., Abashidze, M., Forouhar, F., Benach, J., Zhou, W., Acton, T., Xiao, R., Conover, K., Ma, L.C., Kellie, R., Cunningham, K.E., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 80.61 kDa
Atom Count: 5,393
Modeled Residue Count: 630
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinylglutamate desuccinylase	A, B	350	Vibrio parahaemolyticus	Mutation(s): 6 Gene Names: astE EC: 3.1 (PDB Primary Data), 3.5.1.96 (UniProt)
UniProt
Find proteins for Q87Q40 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87Q40 Go to UniProtKB: Q87Q40
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87Q40
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] mmCIF format, chain C [auth A] mmCIF 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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.267 (Depositor), 0.280 (DCC)
R-Value Work: 0.213 (Depositor), 0.225 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.852	α = 90
b = 72.555	β = 105.66
c = 93.032	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-10-25

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2005-10-25
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.