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- PDB-2zte: MtRuvA Form IV -

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Basic information

Entry
Database: PDB / ID: 2zte
TitleMtRuvA Form IV
ComponentsHolliday junction ATP-dependent DNA helicase ruvA
KeywordsDNA BINDING PROTEIN / RECOMBINATION / branch migration / Holliday junction / DNA binding / oligomerization / acidic pin / ATP-binding / DNA damage / DNA recombination / DNA repair / DNA-binding / Helicase / Hydrolase / Nucleotide-binding / SOS response
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / four-way junction DNA binding / double-strand break repair via homologous recombination / DNA recombination / DNA helicase / DNA repair / DNA damage response ...Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / four-way junction DNA binding / double-strand break repair via homologous recombination / DNA recombination / DNA helicase / DNA repair / DNA damage response / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 ...Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleic acid-binding proteins / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Holliday junction ATP-dependent DNA helicase RuvA / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPrabu, J.R. / Thamotharan, S. / Khanduja, J.S. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA Additional role of RuvB-binding domain and inter species variability
Authors: Prabu, J.R. / Thamotharan, S. / Khanduja, J.S. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
History
DepositionOct 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Holliday junction ATP-dependent DNA helicase ruvA


Theoretical massNumber of molelcules
Total (without water)21,8701
Polymers21,8701
Non-polymers00
Water1086
1
A: Holliday junction ATP-dependent DNA helicase ruvA
x 8


Theoretical massNumber of molelcules
Total (without water)174,9618
Polymers174,9618
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
2
A: Holliday junction ATP-dependent DNA helicase ruvA

A: Holliday junction ATP-dependent DNA helicase ruvA

A: Holliday junction ATP-dependent DNA helicase ruvA

A: Holliday junction ATP-dependent DNA helicase ruvA


Theoretical massNumber of molelcules
Total (without water)87,4804
Polymers87,4804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area6380 Å2
ΔGint-27.6 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.340, 84.340, 100.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Holliday junction ATP-dependent DNA helicase ruvA


Mass: 21870.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ruvA / Plasmid: pMTRA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P66744, UniProt: P9WGW3*PLUS, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystallized in the presence of excess Holliday Junction (1:1.5) with 0.1M sodium succinate, pH5.0, 1.7M ammonium sulfate as the precipitant, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2006 / Details: Mirrors
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→60 Å / Num. obs: 3241 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 12.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 4 / Num. unique all: 468 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H5X

2h5x


Resolution: 3.2→59.637 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3069 316 9.75 %RANDOM
Rwork0.2297 ---
obs0.2297 3240 99.97 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.8723 Å20 Å20 Å2
2--8.8723 Å20 Å2
3----12.6859 Å2
Refinement stepCycle: LAST / Resolution: 3.2→59.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 0 6 980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.5
X-RAY DIFFRACTIONf_dihedral_angle_d17.2
X-RAY DIFFRACTIONf_improper_angle_d1.8
LS refinement shellResolution: 3.2→4.0279 Å
RfactorNum. reflection% reflection
Rfree0.364 165 -
Rwork0.3135 --
obs-1412 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.12770.6862-0.21120.0299-0.59692.6447-0.1659-0.3176-0.06720.0051-0.32580.1448-1.65010.1182-0.18680.3793-0.1298-0.0433-0.13130.02790.21742.786613.760824.268
22.9752-1.82961.53081.5253-1.51460.7949-0.4201-1.06440.95291.03390.0459-0.5878-1.95030.6116-0.06830.8126-0.7109-0.04430.60270.0390.371317.154522.005238.0371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A 1-63
2X-RAY DIFFRACTION2chain A 64-131

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