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- PDB-3io5: Crystal Structure of a dimeric form of the uvsX Recombinase core ... -

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Basic information

Entry
Database: PDB / ID: 3io5
TitleCrystal Structure of a dimeric form of the uvsX Recombinase core domain from Enterobacteria Phage T4
ComponentsRecombination and repair protein
KeywordsDNA BINDING PROTEIN / storage dimer / inactive conformation / RecA like core domain / ATP-binding / DNA damage / DNA recombination / DNA repair / DNA replication / Nucleotide-binding
Function / homology
Function and homology information


ATP-dependent activity, acting on DNA / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / ATP binding
Similarity search - Function
DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Recombination and repair protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsGajewski, S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of the Phage T4 Recombinase UvsX and Its Functional Interaction with the T4 SF2 Helicase UvsW.
Authors: Gajewski, S. / Webb, M.R. / Galkin, V. / Egelman, E.H. / Kreuzer, K.N. / White, S.W.
History
DepositionAug 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Recombination and repair protein
B: Recombination and repair protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0984
Polymers74,9082
Non-polymers1902
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-31 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.974, 95.974, 131.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A22 - 336
2114B22 - 336

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Components

#1: Protein Recombination and repair protein


Mass: 37453.828 Da / Num. of mol.: 2 / Fragment: UNP residues 30-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: fdsA, UVSX / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04529
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate, Ammonium phosphate, DTT, HEPES-Na, pH 8.0, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2008
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 28554 / Num. obs: 28005 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rsym value: 0.059 / Net I/σ(I): 29.5
Reflection shellResolution: 2.35→2.462 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2394 / Rsym value: 0.345 / % possible all: 84.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0035refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→41.56 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.557 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1330 5 %RANDOM
Rwork0.21 ---
obs0.212 26592 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.2 Å2 / Biso mean: 18.079 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 10 55 4287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224319
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.9655838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4565535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8223.352179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.76615737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4851528
X-RAY DIFFRACTIONr_chiral_restr0.1270.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213216
X-RAY DIFFRACTIONr_mcbond_it0.8121.52695
X-RAY DIFFRACTIONr_mcangle_it1.54524341
X-RAY DIFFRACTIONr_scbond_it2.55331624
X-RAY DIFFRACTIONr_scangle_it4.1834.51497
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2039 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.310.5
MEDIUM THERMAL1.062
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 102 -
Rwork0.311 1738 -
all-1840 -
obs--92.79 %
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)
11.8129-1.60420.25153.1237-0.78892.82990.00820.19940.1366-0.0101-0.051-0.0672-0.5423-0.32810.04290.2820.02990.0380.3097-0.00540.0321-20.54433.58979.079
24.3061-2.7088-0.9322.83450.41561.6230.07840.13510.1342-0.05880.0723-0.012-0.10120.0525-0.15070.34010.0570.01850.3783-0.05130.0685-23.06240.466110.415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 335
2X-RAY DIFFRACTION2B23 - 334

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