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- PDB-2g88: MSRECA-dATP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2g88
TitleMSRECA-dATP COMPLEX
ComponentsProtein recA
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 / metal ion binding / cytoplasm
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Protein RecA / Protein RecA
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKrishna, R. / Manjunath, G.P. / Kumar, P. / Surolia, A. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
Citation
Journal: Nucleic Acids Res. / Year: 2006
Title: Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.
Authors: Krishna, R. / Manjunath, G.P. / Kumar, P. / Surolia, A. / 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-AlF4: implications for decreased ATPase activity and molecular aggregation
Authors: Datta, S. / Prabu, M.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.
#3: 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.
History
DepositionMar 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: Protein recA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5435
Polymers37,3441
Non-polymers1,1994
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.212, 108.212, 72.970
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 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) / Gene: recA / Plasmid: PTHIOA / Production host: Escherichia coli (E. coli) / Strain (production host): JC10289 / References: UniProt: Q59560, UniProt: Q7X416*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M citrate phosphate, 30% 4000 PEG, 0.1M sodium citrate, 10% glycerol, 0.1M Nacl, 0.2M ammonium acetate, 0.025 DTT, 0.025 sodium azide, pH 7.0, 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
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→25.4 Å / Num. obs: 7941 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 6.3
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UBC

1ubc


Resolution: 3.2→25.4 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 413864.12 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.309 829 10.6 %RANDOM
Rwork0.237 ---
obs0.237 7829 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.44 Å2 / ksol: 0.11 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.29 Å23.16 Å20 Å2
2---6.29 Å20 Å2
3---12.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.2→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 74 108 2581
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.47
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 124 9.8 %
Rwork0.322 1143 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2d.pard.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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