3DHN | pdb_00003dhn

Crystal structure of the putative epimerase Q89Z24_BACTN from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR310.

PDB DOI: https://doi.org/10.2210/pdb3DHN/pdb

Classification: isomerase, lyase
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-18 Released: 2008-08-12
Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, L.E., Janjua, H., Xiao, R., Acton, T., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.243 (Depositor), 0.260 (DCC)
R-Value Work:
0.232 (Depositor), 0.246 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the putative epimerase Q89Z24_BACTN from Bacteroides thetaiotaomicron.

Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, L.E., Janjua, H., Xiao, R., Acton, T., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 25.64 kDa
Atom Count: 1,784
Modeled Residue Count: 216
Deposited Residue Count: 227
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent epimerase/dehydratase	A	227	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_4553
UniProt
Find proteins for Q89Z24 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89Z24 Go to UniProtKB: Q89Z24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89Z24
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: 2.00 Å
R-Value Free: 0.243 (Depositor), 0.260 (DCC)
R-Value Work: 0.232 (Depositor), 0.246 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.339	α = 90
b = 54.007	β = 90
c = 93.451	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-12

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-08-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary