3HU5 | pdb_00003hu5

CRYSTAL STRUCTURE OF isochorismatase family protein from Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough

PDB DOI: https://doi.org/10.2210/pdb3HU5/pdb

Classification: HYDROLASE
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-06-12 Released: 2009-06-30
Deposition Author(s): Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.225 (Depositor), 0.229 (DCC)
R-Value Work:
0.187 (Depositor), 0.191 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF isochorismatase family protein from Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough

Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 44.09 kDa
Atom Count: 3,196
Modeled Residue Count: 380
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isochorismatase family protein	A, B	204	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 Gene Names: DVU_0033
UniProt
Find proteins for Q72G28 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72G28 Go to UniProtKB: Q72G28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72G28
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.50 Å
R-Value Free: 0.225 (Depositor), 0.229 (DCC)
R-Value Work: 0.187 (Depositor), 0.191 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.663	α = 90
b = 116.79	β = 90
c = 105.661	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Malashkevich, V.N.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2012-10-24
Changes: Structure summary
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2018-11-21
Changes: Data collection, Structure summary
Version 1.5: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2024-10-16
Changes: Data collection, Database references, 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.