1UBG | pdb_00001ubg

MsREcA-dATP complex

PDB DOI: https://doi.org/10.2210/pdb1UBG/pdb

Classification: RECOMBINATION
Organism(s): Mycolicibacterium smegmatis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-04-04 Released: 2003-07-22
Deposition Author(s): Datta, S., Krishna, R., Ganesh, N., Chandra, N.R., Muniyappa, K., Vijayan, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.286 (Depositor), 0.279 (DCC)
R-Value Work:
0.222 (Depositor), 0.218 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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Literature

Crystal Structures of Mycobacterium smegmatis RecA and Its Nucleotide Complexes

Datta, S., Krishna, R., Ganesh, N., Chandra, N.R., Muniyappa, K., Vijayan, M.

(2003) J Bacteriol 185: 4280-4284

PubMed: 12837805 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/JB.185.14.4280-4284.2003
Primary Citation Related Structures:
1UBC, 1UBE, 1UBF, 1UBG

PubMed Abstract:
The crystal structures of Mycobacterium smegmatis RecA (RecA(Ms)) and its complexes with ADP, ATPgammaS, and dATP show that RecA(Ms) has an expanded binding site like that in Mycobacterium tuberculosis RecA, although there are small differences between the proteins in their modes of nucleotide binding. Nucleotide binding is invariably accompanied by the movement of Gln 196, which appears to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding loops. These observations provide a framework for exploring the known properties of the RecA proteins.

Organizational Affiliation

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Macromolecule Content

Total Structure Weight: 37.84 kDa
Atom Count: 2,486
Modeled Residue Count: 330
Deposited Residue Count: 349
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RecA	A	349	Mycolicibacterium smegmatis	Mutation(s): 0
UniProt
Find proteins for Q59560 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore Q59560 Go to UniProtKB: Q59560
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59560
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTP Query on DTP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.286 (Depositor), 0.279 (DCC)
R-Value Work: 0.222 (Depositor), 0.218 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.96	α = 90
b = 102.96	β = 90
c = 73.578	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-07-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-07-22
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description