1VP7 | pdb_00001vp7

Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VP7/pdb

Classification: HYDROLASE
Organism(s): Bordetella pertussis Tohama I
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-10-14 Released: 2004-10-26
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.244 (Depositor), 0.244 (DCC)
R-Value Work:
0.203 (Depositor), 0.205 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1VP7

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Exodeoxyribonuclease VII small subunit E.C.3.1.11.6 (NP_881400.1) from Bordetella pertussis at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 67.39 kDa
Atom Count: 3,262
Modeled Residue Count: 417
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exodeoxyribonuclease VII small subunit	A, B, C, D, E A, B, C, D, E, F	100	Bordetella pertussis Tohama I	Mutation(s): 2 Gene Names: NP_881400.1 EC: 3.1.11.6
UniProt
Find proteins for Q7VV85 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VV85 Go to UniProtKB: Q7VV85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7VV85
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.244 (Depositor), 0.244 (DCC)
R-Value Work: 0.203 (Depositor), 0.205 (DCC)
R-Value Observed: 0.205 (Depositor)

Diffraction Data:

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.03	α = 90
b = 107.03	β = 90
c = 207.26	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	model building
autoSHARP	phasing
REFMAC	refinement
CCP4	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-10-26

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-10-26
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, 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.