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- PDB-2ztc: MtRuvA Form II -

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Basic information

Entry
Database: PDB / ID: 2ztc
TitleMtRuvA Form II
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 / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / 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 / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / 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: 2.8 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: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
C: Holliday junction ATP-dependent DNA helicase ruvA
D: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8498
Polymers87,4804
Non-polymers3684
Water86548
1
A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
C: Holliday junction ATP-dependent DNA helicase ruvA
D: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules

A: Holliday junction ATP-dependent DNA helicase ruvA
B: Holliday junction ATP-dependent DNA helicase ruvA
C: Holliday junction ATP-dependent DNA helicase ruvA
D: Holliday junction ATP-dependent DNA helicase ruvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,69716
Polymers174,9618
Non-polymers7378
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area23620 Å2
ΔGint-166.3 kcal/mol
Surface area64830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.200, 95.669, 77.209
Angle α, β, γ (deg.)90.00, 121.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A -5-131
211chain B -5-131
311chain C -5-131
411chain D -5-131

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Components

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


Mass: 21870.078 Da / Num. of mol.: 4
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystallized using 0.1M sodium succinate, pH5.5, 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: Nov 10, 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: 2.8→30 Å / Num. obs: 19886 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 57.79 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1959 / % possible all: 95.8

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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: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 979 5.16 %RANDOM
Rwork0.2293 ---
obs0.2293 18969 91.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7912 Å2-0 Å2-4.1236 Å2
2---13.9331 Å20 Å2
3----5.6761 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5300 0 24 48 5372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.3
X-RAY DIFFRACTIONf_improper_angle_d2.2
X-RAY DIFFRACTIONf_dihedral_angle_d16.6
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A984X-RAY DIFFRACTIONPOSITIONAL
12B984X-RAY DIFFRACTIONPOSITIONAL0.05
13C984X-RAY DIFFRACTIONPOSITIONAL0.051
14D973X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shellResolution: 2.8→2.9187 Å /
Num. reflection% reflection
Rfree152 -
obs2364 85 %
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)
14.0099-0.83141.73521.4449-0.70841.60261.0995-0.1071-0.8522-0.2217-0.42730.02570.641-0.1249-0.53810.2328-0.044-0.19530.09790.00640.2502-5.718536.505-32.1917
20.0050.72150.01541.05240.3842-0.06350.3665-0.281-0.34490.8973-0.4894-0.9162-0.05280.01440.07880.5599-0.3872-0.5580.41560.46910.740714.195527.3111-12.8651
30.8691-0.1247-0.3615.12323.131.82230.52480.03870.0303-0.577-0.681-0.1243-0.4881-0.49260.06360.48160.08820.05860.4050.01080.23951.694764.299-25.7867
41.80270.30080.7633-0.01970.09390.41991.0705-0.7675-0.60030.3992-0.4758-0.13530.4478-0.2631-0.39340.904-0.5123-0.33380.43290.21240.265821.171454.7477-6.4071
50.7804-0.05070.17110.2414-0.29690.33850.0743-0.0554-0.12830.3382-0.3967-0.2489-0.14920.24880.1708-0.194-0.8733-0.2678-0.6140.3830.39587.03389.7351-18.1654
61.08550.28570.21320.7028-0.23451.10231.1761-1.3986-1.08560.4378-0.4666-0.19970.3149-0.4891-0.64021.0769-0.6948-0.71760.84120.50630.704732.882145.11996.5851
72.0647-0.49240.11422.31070.0669-0.3340.2757-0.3455-0.1471-0.6522-0.31460.72210.0301-0.05010.14610.30590.1466-0.2310.2376-0.16230.3893-19.943745.4142-42.4869
80.21080.51090.44383.7775-0.20010.61610.2851-0.1955-0.27070.8282-0.9239-0.57970.00770.07320.46960.372-0.2145-0.08480.35210.0510.48178.109981.7903-18.2045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A 1-132
2X-RAY DIFFRACTION2chain B 1-132
3X-RAY DIFFRACTION3chain C 1-132
4X-RAY DIFFRACTION4chain D 1-132
5X-RAY DIFFRACTION5chain A 146-195
6X-RAY DIFFRACTION6chain B 146-195
7X-RAY DIFFRACTION7chain C 146-195
8X-RAY DIFFRACTION8chain D 146-195

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