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- PDB-1mo4: RECA-ATP-GAMMA-S COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1mo4
TitleRECA-ATP-GAMMA-S COMPLEX
ComponentsRecA
KeywordsHYDROLASE / RECOMBINATION / DNA-REPAIR / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


DNA strand invasion / DNA strand exchange activity / UV protection / intron homing / intein-mediated protein splicing / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity ...DNA strand invasion / DNA strand exchange activity / UV protection / intron homing / intein-mediated protein splicing / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity / single-stranded DNA binding / manganese ion binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / response to antibiotic / DNA repair / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / LAGLIDADG-like domain / 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 protein, C-terminal domain / Rec A Protein; domain 2 / LAGLIDADG-like domain / 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 N-terminal domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Protein RecA / Protein RecA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDatta, S. / Ganesh, N. / Chandra, N.R. / TB Structural Genomics Consortium (TBSGC)
Citation
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.
#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. / Vaze, M.B. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#2: Journal: Biochemistry / Year: 1996
Title: Functional Characterization of the Precursor and Spliced Forms of Reca Protein of Mycobacterium Tuberculosis.
Authors: Ajay Kumar, R. / Vaze, M. / Chandra, N.R. / Vijayan, M. / Muniyappa, K.
History
DepositionSep 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Non-polymer description
Revision 1.4Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Oct 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)37,7462
Polymers37,2221
Non-polymers5231
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.075, 108.075, 72.545
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: 37222.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pEJ135 / Production host: Escherichia coli (E. coli) / Strain (production host): KM4104
References: UniProt: P0A5U4, UniProt: P9WHJ3*PLUS, EC: 3.4.99.37
#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.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE CORRESPONDS TO THE MATURE MTRECA, A 38 KD POLYPEPTIDE CHAIN WHICH IS AN AUTOSPLICED ...THIS STRUCTURE CORRESPONDS TO THE MATURE MTRECA, A 38 KD POLYPEPTIDE CHAIN WHICH IS AN AUTOSPLICED PRODUCT OF THE 85 KD MTRECA PRECURSOR (P0A5U4). THE MATURE MTRECA IS MADE OF RESIDUES 1-254 AND 695-790 OF THE PRECURSOR, RESULTING IN A SINGLE CHAIN OF 350 AA. FOR ANY RESIDUE N IN MTRECA SEQUENCE, N-1 WILL GIVE THE CORRESPONDING NUMBER IN ECRECA SEQUENCE.

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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: 3.219 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, TRIS ACETATE, NACL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMTris-acetate1droppH7.
3100 mM1dropNaCl
46 %PEG40001drop
520 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 12, 2000 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 8054 / Num. obs: 8054 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.5
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / Num. unique all: 790 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 40215
Reflection shell
*PLUS
Highest resolution: 3.2 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G19

1g19


Resolution: 3.2→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 107770.79 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 807 10.7 %RANDOM
Rwork0.201 ---
all0.207 8054 --
obs0.207 7523 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.301 Å2 / ksol: 0.288989 e/Å3
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1--4.34 Å21.03 Å20 Å2
2---4.34 Å20 Å2
3---8.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 31 70 2446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 105 9.2 %
Rwork0.291 1034 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SAP_XPLOR.PARAMSAP_XPLOR.TOP
Refinement
*PLUS
Highest resolution: 3.2 Å / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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