2D4G

Structure of YjcG protein, a putative 2'-5' RNA ligase from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb2D4G/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-10-19 Released: 2006-10-17
Deposition Author(s): Li, D., Liang, Y.H., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.264
R-Value Work: 0.224
R-Value Observed: 0.235

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of B. subtilis YjcG characterizing the YjcG-like group of 2H phosphoesterase superfamily.

Li, D., Liu, C., Liang, Y.H., Li, L.F., Su, X.D.

(2008) Proteins 72: 1071-1076

PubMed: 18473364 Search on PubMed
DOI: https://doi.org/10.1002/prot.22093
Primary Citation of Related Structures:
2D4G

Organizational Affiliation

National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

Macromolecule Content

Total Structure Weight: 39.65 kDa
Atom Count: 2,970
Modelled Residue Count: 336
Deposited Residue Count: 342
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 BSU11850	A, B	171	Bacillus subtilis	Mutation(s): 0
UniProt
Find proteins for O31629 (Bacillus subtilis (strain 168)) Explore O31629 Go to UniProtKB: O31629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O31629
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: 2.30 Å
R-Value Free: 0.264
R-Value Work: 0.224
R-Value Observed: 0.235
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.66	α = 90
b = 73.93	β = 113.56
c = 61.77	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-10-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-10-17
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: 2013-11-27
Changes: Database references
Version 1.4: 2017-10-11
Changes: Refinement description

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 R01GM133198.