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- PDB-4ppf: Mycobacterium tuberculosis RecA citrate bound low temperature str... -

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Basic information

Entry
Database: PDB / ID: 4ppf
TitleMycobacterium tuberculosis RecA citrate bound low temperature structure IIA-N
ComponentsProtein RecA, 1st part, 2nd part
KeywordsHYDROLASE / HOMOLOGOUS RECOMBINATION / DNA REPAIR / ATPASE / RECOMBINASE / DNA BINDING PROTEIN / PLOOP CONTAINING NTPASE FOLD / ATP BINDING / HYDROLYSIS
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
CITRATE ANION / Protein RecA / Protein RecA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChandran, A.V. / Prabu, J.R. / Patil, N.K. / Muniyappa, K. / Vijayan, M.
Citation
Journal: J.Biosci. / Year: 2015
Title: Structural studies on Mycobacterium tuberculosis RecA: Molecular plasticity and interspecies variability
Authors: Chandran, A.V. / Prabu, J.R. / Nautiyal, A. / Patil, K.N. / Muniyappa, K. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes
Authors: Prabu, J.R. / Manjunath, G.P. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#2: 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.
#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.
#4: 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.
#5: 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.M. / Vaze, M.B. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_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, 1st part, 2nd part
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7068
Polymers37,2221
Non-polymers4837
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.020, 107.020, 70.270
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, 1st part, 2nd part / Recombinase A


Mass: 37222.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2806, MTV002.02c, recA, Rv2737c / Plasmid: PEJ135 / Production host: Escherichia coli (E. coli) / Strain (production host): KM4104
References: UniProt: P0A5U4, UniProt: P9WHJ3*PLUS, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN IS EXPRESSED AS A 790 AMINO ACID RESIDUE PRECURSOR (UNIPROT P0A5U4). ONCE IT IS ...THE PROTEIN IS EXPRESSED AS A 790 AMINO ACID RESIDUE PRECURSOR (UNIPROT P0A5U4). ONCE IT IS RELEASED INTO THE CELL, THE CHAIN MTU RECA INTEIN (RESIDUES 252-691) IS CLEAVED OFF, CHAINS 1ST PART (RESIDUES 1-251) AND 2ND PART (RESIDUES 692-790) JOIN TOGETHER TO FORM THE MATURE PROTEIN.

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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: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 15% PEG 3350, 10% PEG 5000 MME, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2013 / Details: Bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→46.34 Å / Num. obs: 19963 / Redundancy: 10.5 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2 / Num. unique all: 2835

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G19

1g19


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.043 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23478 2053 10.3 %RANDOM
Rwork0.18441 ---
obs0.18938 17909 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.901 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.16 Å20 Å2
2---0.16 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 31 110 2404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192317
X-RAY DIFFRACTIONr_bond_other_d0.0010.022249
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9883123
X-RAY DIFFRACTIONr_angle_other_deg0.73235166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4925.21792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88515392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5851514
X-RAY DIFFRACTIONr_chiral_restr0.0670.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 149 -
Rwork0.296 1284 -
obs--94.4 %

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