2D4G | pdb_00002d4g

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 (Depositor), 0.269 (DCC)
R-Value Work:
0.224 (Depositor), 0.237 (DCC)
R-Value Observed:
0.235 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2D4G

This is version 1.5 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 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
Modeled Residue Count: 336
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein BSU11850	A, B	171	Bacillus subtilis	Mutation(s): 0 EC: 3.1
UniProt
Find proteins for O31629 (Bacillus subtilis (strain 168)) Explore O31629 Go to UniProtKB: O31629
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.269 (DCC)
R-Value Work: 0.224 (Depositor), 0.237 (DCC)
R-Value Observed: 0.235 (Depositor)

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

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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
Version 1.5: 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.