3HLU | pdb_00003hlu

Crystal Structure of Uncharacterized Protein Conserved in Bacteria DUF2179 from Eubacterium ventriosum

PDB DOI: https://doi.org/10.2210/pdb3HLU/pdb

Classification: structural genomics, unknown function
Organism(s): Eubacterium ventriosum ATCC 27560
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-05-28 Released: 2009-07-07
Deposition Author(s): Kim, Y., Li, H., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.252 (Depositor), 0.254 (DCC)
R-Value Work:
0.226 (Depositor), 0.224 (DCC)
R-Value Observed:
0.227 (Depositor)

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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Uncharacterized Protein Conserved in Bacteria DUF2179 from Eubacterium ventriosum

Kim, Y., Li, H., Keigher, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 22.16 kDa
Atom Count: 1,174
Modeled Residue Count: 146
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein DUF2179	A, B	96	Eubacterium ventriosum ATCC 27560	Mutation(s): 0 Gene Names: EUBVEN_01903
UniProt
Find proteins for A5Z863 (Eubacterium ventriosum ATCC 27560) Explore A5Z863 Go to UniProtKB: A5Z863
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5Z863
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: 2.65 Å
R-Value Free: 0.252 (Depositor), 0.254 (DCC)
R-Value Work: 0.226 (Depositor), 0.224 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.588	α = 90
b = 63.392	β = 90
c = 82.197	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, 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.