1ZP6

Crystal Structure of Atu3015, a Putative Cytidylate Kinase from Agrobacterium tumefaciens, Northeast Structural Genomics Target AtR62

PDB DOI: https://doi.org/10.2210/pdb1ZP6/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-05-16 Released: 2005-05-24
Deposition Author(s): Forouhar, F., Abashidze, M., Vorobiev, S.M., Kuzin, A., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.322
R-Value Work: 0.253
R-Value Observed: 0.253

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Atu3015, a Putative Cytidylate Kinase from Agrobacterium tumefaciens, Northeast Structural Genomics Target AtR62

Forouhar, F., Abashidze, M., Vorobiev, S.M., Kuzin, A., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 21.21 kDa
Atom Count: 1,365
Modelled Residue Count: 176
Deposited Residue Count: 191
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 Atu3015	A	191	Agrobacterium fabrum str. C58	Mutation(s): 2
UniProt
Find proteins for A9CEJ3 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CEJ3 Go to UniProtKB: A9CEJ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CEJ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 3.20 Å
R-Value Free: 0.322
R-Value Work: 0.253
R-Value Observed: 0.253
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.96	α = 90
b = 91.96	β = 90
c = 173.603	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SDMS	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-05-24

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2005-05-24
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-11-16
Changes: Atomic model
Version 1.4: 2017-10-11
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.