4IM9 | pdb_00004im9

Cystal structure of DnaG primase C-terminal domain from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb4IM9/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-01-02 Released: 2014-05-07
Deposition Author(s): Abdul Rehman, S.A., Tarique, K.F., Gourinath, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.264 (Depositor), 0.262 (DCC)
R-Value Work:
0.227 (Depositor), 0.231 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cystal structure of DnaG primase C-terminal domain from Vibrio cholerae

Abdul Rehman, S.A., Tarique, K.F., Gourinath, S.

To be published.

Macromolecule Content

Total Structure Weight: 53.12 kDa
Atom Count: 3,286
Modeled Residue Count: 401
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase	A, B, C	152	Vibrio cholerae O395	Mutation(s): 0 Gene Names: C-terminal domain, dnaG, Primase, VC395_0535 EC: 2.7.7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.264 (Depositor), 0.262 (DCC)
R-Value Work: 0.227 (Depositor), 0.231 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.412	α = 90
b = 73.779	β = 90
c = 132.653	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Abdul Rehman, S.A.

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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.