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- PDB-1cuk: ESCHERICHIA COLI RUVA PROTEIN AT PH 4.9 AND ROOM TEMPERATURE -

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Basic information

Entry
Database: PDB / ID: 1cuk
TitleESCHERICHIA COLI RUVA PROTEIN AT PH 4.9 AND ROOM TEMPERATURE
ComponentsRUVA PROTEIN
KeywordsHELICASE / DNA REPAIR / SOS RESPONSE / DNA-BINDING / DNA RECOMBINATION
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / SOS response / recombinational repair / four-way junction DNA binding / response to radiation / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Bacterial DNA recombination protein RuvA / 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 / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 ...Bacterial DNA recombination protein RuvA / 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 / 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 branch migration complex subunit RuvA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsRafferty, J.B. / Rice, D.W.
Citation
Journal: Science / Year: 1996
Title: Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction.
Authors: Rafferty, J.B. / Sedelnikova, S.E. / Hargreaves, D. / Artymiuk, P.J. / Baker, P.J. / Sharples, G.J. / Mahdi, A.A. / Lloyd, R.G. / Rice, D.W.
#1: Journal: To be Published
Title: Crystallization of E.Coli Ruva Gives Insights Into the Symmetry of a Holliday Junction/Protein Complex
Authors: Sedelnikova, S.E. / Rafferty, J.B. / Hargreaves, D. / Mahdi, A.A. / Lloyd, R.G. / Rice, D.W.
History
DepositionAug 28, 1996Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUVA PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,1981
Polymers22,1981
Non-polymers00
Water91951
1
A: RUVA PROTEIN

A: RUVA PROTEIN

A: RUVA PROTEIN

A: RUVA PROTEIN


Theoretical massNumber of molelcules
Total (without water)88,7914
Polymers88,7914
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 area9540 Å2
ΔGint-53 kcal/mol
Surface area33420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.700, 83.700, 33.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein RUVA PROTEIN


Mass: 22197.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 12 BL21 (DE3) / Cell line: BL21 / Plasmid: PAM159 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A809
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 53 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Sedelnikova, S.E., (1999) Acta Crystallogr. D., 55, 263.
PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
20.1 Mimidazole-HCl1drop
30.70-0.95 Msodium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 26, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 16391 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.073

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
RefinementResolution: 1.9→15 Å / σ(F): 0
Details: THE B-FACTORS FOR THE C-TERMINAL SEGMENT OF THE PROTEIN (RESIDUES 107 - 203) ARE HIGH WITH AN AVERAGE VALUE OF 73.6 A**2 OVER ALL ATOMS (71.0A**2 FOR MAIN CHAIN) AND THUS REPRESENT ...Details: THE B-FACTORS FOR THE C-TERMINAL SEGMENT OF THE PROTEIN (RESIDUES 107 - 203) ARE HIGH WITH AN AVERAGE VALUE OF 73.6 A**2 OVER ALL ATOMS (71.0A**2 FOR MAIN CHAIN) AND THUS REPRESENT POSITIONAL UNCERTAINTY OF APPROXIMATELY 1A IN SOME REGIONS.
RfactorNum. reflection
Rwork0.209 -
obs-17090
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1377 0 0 51 1428
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0160.3
X-RAY DIFFRACTIONt_angle_deg1.91
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0085
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.209 / Rfactor Rfree: 0.027
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.008 / Weight: 5

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