2OZV | pdb_00002ozv

Crystal structure of a predicted O-methyltransferase, protein Atu636 from Agrobacterium tumefaciens.

PDB DOI: https://doi.org/10.2210/pdb2OZV/pdb

Classification: TRANSFERASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-02-27 Released: 2007-03-27
Deposition Author(s): Cuff, M.E., Xu, X., Zheng, X., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.214 (Depositor), 0.222 (DCC)
R-Value Work:
0.178 (Depositor), 0.189 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The structure of a predicted O-methyltransferase, protein Atu636 from Agrobacterium tumefaciens.

Cuff, M.E., Xu, X., Zheng, X., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 57.33 kDa
Atom Count: 4,033
Modeled Residue Count: 418
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein Atu0636	A, B	260	Agrobacterium fabrum str. C58	Mutation(s): 9 Gene Names: Atu0636
UniProt
Find proteins for Q7D120 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D120 Go to UniProtKB: Q7D120
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7D120
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: 1.70 Å
R-Value Free: 0.214 (Depositor), 0.222 (DCC)
R-Value Work: 0.178 (Depositor), 0.189 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.544	α = 90
b = 78.054	β = 94.55
c = 62.261	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-03-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-03-27
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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.