3DXQ

Crystal structure of choline/ethanolamine kinase family protein (NP_106042.1) from MESORHIZOBIUM LOTI at 2.55 A resolution

PDB DOI: https://doi.org/10.2210/pdb3DXQ/pdb

Classification: TRANSFERASE
Organism(s): Mesorhizobium loti
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-24 Released: 2008-08-05
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.284
R-Value Work: 0.242
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of choline/ethanolamine kinase family protein (NP_106042.1) from MESORHIZOBIUM LOTI at 2.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 67.27 kDa
Atom Count: 4,467
Modelled Residue Count: 586
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
choline/ethanolamine kinase family protein	A, B	301	Mesorhizobium loti	Mutation(s): 0 Gene Names: NP_106042.1, mll5367
UniProt
Find proteins for Q98BZ3 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98BZ3 Go to UniProtKB: Q98BZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q98BZ3
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: 2.55 Å
R-Value Free: 0.284
R-Value Work: 0.242
R-Value Observed: 0.244
Space Group: P 2₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M33DXQ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.07	α = 90
b = 173.62	β = 90
c = 39.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-05
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

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.