3G6S | pdb_00003g6s

Crystal structure of the endonuclease/exonuclease/phosphatase (BVU_0621) from Bacteroides vulgatus. Northeast Structural Genomics Consortium Target BvR56D

PDB DOI: https://doi.org/10.2210/pdb3G6S/pdb

Classification: HYDROLASE
Organism(s): Phocaeicola vulgatus ATCC 8482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-08 Released: 2009-02-17
Deposition Author(s): Forouhar, F., Lew, S., Seetharaman, J., Xiao, R., Sahdev, S., Foote, E.L., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.234 (Depositor), 0.223 (DCC)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the endonuclease/exonuclease/phosphatase (BVU_0621) from Bacteroides vulgatus.

Forouhar, F., Lew, S., Seetharaman, J., Xiao, R., Sahdev, S., Foote, E.L., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 30.88 kDa
Atom Count: 2,182
Modeled Residue Count: 261
Deposited Residue Count: 267
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative endonuclease/exonuclease/phosphatase family protein	A	267	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0 Gene Names: BVU_0621
UniProt
Find proteins for A6KY15 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6KY15 Go to UniProtKB: A6KY15
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6KY15
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.234 (Depositor), 0.223 (DCC)
R-Value Work: 0.180 (Depositor)
R-Value Observed: 0.180 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.601	α = 90
b = 75.601	β = 90
c = 66.715	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXD	phasing
SOLVE	phasing
RESOLVE	model building
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-02-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary