2QZU | pdb_00002qzu

Crystal structure of the putative sulfatase yidJ from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR123

PDB DOI: https://doi.org/10.2210/pdb2QZU/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis YCH46
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-08-17 Released: 2007-09-04
Deposition Author(s): Vorobiev, S.M., Abashidze, M., Seetharaman, J., Wang, D., Cunningham, K., Maglaqui, M., Owens, L., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.217 (Depositor), 0.231 (DCC)
R-Value Work:
0.195 (Depositor), 0.209 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

X-ray crystal structure of the putative sulfatase yidJ from Bacteroides fragilis.

Vorobiev, S.M., Abashidze, M., Seetharaman, J., Wang, D., Cunningham, K., Maglaqui, M., Owens, L., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 57.23 kDa
Atom Count: 4,184
Modeled Residue Count: 465
Deposited Residue Count: 491
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sulfatase yidJ	A	491	Bacteroides fragilis YCH46	Mutation(s): 0 Gene Names: BF0881
UniProt
Find proteins for Q64XZ4 (Bacteroides fragilis (strain YCH46)) Explore Q64XZ4 Go to UniProtKB: Q64XZ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q64XZ4
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: 1.70 Å
R-Value Free: 0.217 (Depositor), 0.231 (DCC)
R-Value Work: 0.195 (Depositor), 0.209 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.894	α = 90
b = 82.336	β = 90
c = 89.359	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-04

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-09-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary