3DNH | pdb_00003dnh

The crystal structure of the protein Atu2129 (unknown function) from Agrobacterium tumefaciens str. C58

PDB DOI: https://doi.org/10.2210/pdb3DNH/pdb

Classification: structural genomics, unknown function
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-02 Released: 2008-09-02
Deposition Author(s): Tan, K., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.238 (Depositor), 0.269 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3DNH

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

Literature

The crystal structure of the protein Atu2129 (unknown function) from Agrobacterium tumefaciens str. C58

Tan, K., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 55.46 kDa
Atom Count: 3,843
Modeled Residue Count: 467
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein Atu2129	A, B	258	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: AGR_C_3862, Atu2129
UniProt
Find proteins for A9CI98 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CI98 Go to UniProtKB: A9CI98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9CI98
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: 1.94 Å
R-Value Free: 0.238 (Depositor), 0.269 (DCC)
R-Value Work: 0.187 (Depositor)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.651	α = 90
b = 66.83	β = 108.19
c = 69.967	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-09-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-10-30
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.