3CUC | pdb_00003cuc

CRYSTAL STRUCTURE OF A FIC DOMAIN CONTAINING SIGNALING PROTEIN (BT_2513) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.71 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3CUC/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-04-16 Released: 2008-04-29
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.248 (Depositor), 0.238 (DCC)
R-Value Work:
0.222 (Depositor)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Protein of Unknown Function with a Fic Domain (NP_811426.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.71 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 67.15 kDa
Atom Count: 4,226
Modeled Residue Count: 530
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein of unknown function with a Fic domain	A, B	291	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: NP_811426.1, BT_2513
UniProt
Find proteins for Q8A4T4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A4T4 Go to UniProtKB: Q8A4T4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A4T4
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: 2.71 Å
R-Value Free: 0.248 (Depositor), 0.238 (DCC)
R-Value Work: 0.222 (Depositor)
R-Value Observed: 0.224 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.725	α = 90
b = 138.725	β = 90
c = 120.723	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-04-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references
Version 1.5: 2024-10-30
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.