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- PDB-1ubf: MsREcA-ATPgS complex -

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Basic information

Entry
Database: PDB / ID: 1ubf
TitleMsREcA-ATPgS complex
ComponentsRecA
KeywordsRECOMBINATION / DNA-REPAIR
Function / homology
Function and homology information


SOS response / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : / recA bacterial DNA recombination protein ...RecA protein, C-terminal domain / Rec A Protein; domain 2 / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : / recA bacterial DNA recombination protein / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Protein RecA
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsDatta, S. / Krishna, R. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
Citation
Journal: J.BACTERIOL. / Year: 2003
Title: Crystal Structures of Mycobacterium smegmatis RecA and Its Nucleotide Complexes
Authors: Datta, S. / Krishna, R. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#1: Journal: Nucleic Acids Res. / Year: 2000
Title: Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation
Authors: Datta, S. / Prabu, M. / Vaze, M.B. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#2: Journal: Proteins / Year: 2003
Title: Structural studies on MtRecA-nucleotide complexes: Insights into DNA and nucleotide binding and the structural signature of NTP recognition
Authors: Datta, S. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
History
DepositionApr 4, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Non-polymer description
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RecA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8682
Polymers37,3441
Non-polymers5231
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.275, 103.275, 73.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein RecA / Recombinase A


Mass: 37344.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Plasmid: pThioA / Production host: Escherichia coli (E. coli) / Strain (production host): JC10289 / References: UniProt: Q59560
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.017522 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, CIT-PHOS, NACL, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 5683 / Num. obs: 5464 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.103 / Net I/σ(I): 6.7
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.1 / Num. unique all: 503 / % possible all: 89.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g19

1g19


Resolution: 3.5→14.93 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 205540.2 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 517 10.3 %RANDOM
Rwork0.217 ---
all0.23 5626 --
obs0.217 4996 88.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.147575 e/Å3
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1--14.84 Å20.19 Å20 Å2
2---14.84 Å20 Å2
3---29.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 3.5→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 31 43 2338
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.392
X-RAY DIFFRACTIONc_angle_deg3.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.72
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 65 9.5 %
Rwork0.313 621 -
obs-621 73.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SAP.PARAMSAP.TOP

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