4MQD | pdb_00004mqd

Crystal structure of ComJ, inhibitor of the DNA degrading activity of NucA, from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb4MQD/pdb

Classification: Hydrolase Inhibitor
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-09-16 Released: 2013-10-09
Deposition Author(s): Chang, C., Mack, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.240 (Depositor), 0.212 (DCC)
R-Value Work:
0.178 (Depositor)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4MQD

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of ComJ, inhibitor of the DNA degrading activity of NucA, from Bacillus subtilis

Chang, C., Mack, J., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 61.89 kDa
Atom Count: 4,562
Modeled Residue Count: 530
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-entry nuclease inhibitor	A, B, C, D	135	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: nin, comJ, BSU03420
UniProt
Find proteins for P12669 (Bacillus subtilis (strain 168)) Explore P12669 Go to UniProtKB: P12669
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12669
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.240 (Depositor), 0.212 (DCC)
R-Value Work: 0.178 (Depositor)
R-Value Observed: 0.181 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.826	α = 90
b = 125.826	β = 90
c = 37.013	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-09

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-10-09
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 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.