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- PDB-4oqf: Mycobacterium tuberculosis RecA glycerol bound low temperature st... -

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Basic information

Entry
Database: PDB / ID: 4oqf
TitleMycobacterium tuberculosis RecA glycerol bound low temperature structure IIB-SR
ComponentsProtein RecA
KeywordsDNA BINDING PROTEIN / HOMOLOGOUS RECOMBINATION / DNA REPAIR / ATPASE / 'P-LOOP CONTAINING NTPASE' FOLD / HYDROLYSIS / ATP BINDING
Function / homology
Function and homology information


DNA strand invasion / DNA strand exchange activity / UV protection / intein-mediated protein splicing / intron homing / 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 / intein-mediated protein splicing / intron homing / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity / manganese ion binding / single-stranded DNA 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 / cytosol / cytoplasm
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 bacterial DNA recombination protein / 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. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / 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
Protein RecA / Protein RecA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 2, 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 / 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: Protein RecA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5284
Polymers35,3121
Non-polymers2163
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.840, 106.840, 70.610
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 / Endonuclease PI-MtuI / Mtu RecA intein


Mass: 35312.215 Da / Num. of mol.: 1 / Fragment: UNP residues 1-252, UNP residues 693-771
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT ONCE A CHAIN (790 AMINO ACIDS, FULL LENGTH) IS RELEASED INTO THE CELL, THE CHAIN ...AUTHORS STATE THAT ONCE A CHAIN (790 AMINO ACIDS, FULL LENGTH) IS RELEASED INTO THE CELL, THE CHAIN IS CLEAVED OFF AND THE PEPTIDE STRETCHES 1-251 AND 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: 3.29 Å3/Da / Density % sol: 62.66 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / pH: 5.8
Details: 15% PEG3350, 10% PEG5000 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2012 / Details: MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.8→70.61 Å / Num. obs: 11452 / Redundancy: 11.9 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 16.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 11 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 2.9

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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: 1G19

1g19


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.027 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.825 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25359 1129 9.9 %RANDOM
Rwork0.19347 ---
obs0.19924 10300 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.44 Å20 Å2
2---0.44 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 14 63 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192265
X-RAY DIFFRACTIONr_bond_other_d0.0010.022192
X-RAY DIFFRACTIONr_angle_refined_deg0.981.9853056
X-RAY DIFFRACTIONr_angle_other_deg0.68635033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0495307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48325.69886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741511
X-RAY DIFFRACTIONr_chiral_restr0.0510.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02448
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 73 -
Rwork0.272 764 -
obs--100 %

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