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- PDB-3vcf: SSV1 integrase C-terminal catalytic domain (174-335aa) -

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Basic information

Entry
Database: PDB / ID: 3vcf
TitleSSV1 integrase C-terminal catalytic domain (174-335aa)
ComponentsProbable integrase
KeywordsRECOMBINATION / catalyzes site-specific integration
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity / symbiont entry into host cell / DNA binding
Similarity search - Function
ORF D-335-like / Integrase SSV1, C-terminal / ORF D-335-like protein / Archaeal phage integrase / Intergrase catalytic core / hpI Integrase; Chain A / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. ...ORF D-335-like / Integrase SSV1, C-terminal / ORF D-335-like protein / Archaeal phage integrase / Intergrase catalytic core / hpI Integrase; Chain A / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSulfolobus virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOuyang, S. / Liang, W. / Huang, L. / Liu, Z.-J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase.
Authors: Zhan, Z. / Ouyang, S. / Liang, W. / Zhang, Z. / Liu, Z.J. / Huang, L.
History
DepositionJan 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable integrase
B: Probable integrase


Theoretical massNumber of molelcules
Total (without water)38,5072
Polymers38,5072
Non-polymers00
Water2,162120
1
A: Probable integrase


Theoretical massNumber of molelcules
Total (without water)19,2541
Polymers19,2541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable integrase


Theoretical massNumber of molelcules
Total (without water)19,2541
Polymers19,2541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.051, 89.051, 147.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-437-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.128838, -0.737981, -0.662408), (-0.665979, 0.430536, -0.609189), (0.734761, 0.519637, -0.43601)45.26682, 63.46315, -19.57064

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Components

#1: Protein Probable integrase


Mass: 19253.510 Da / Num. of mol.: 2 / Fragment: C-terminal domain (residues 174-335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus virus 1 / Gene: d335 / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P20214
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.056M NaH2PO4, 1.35M K2HPO4, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→34.11 Å / Num. obs: 16941 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 31.45 Å2
Reflection shellResolution: 2.7→2.95 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→34.11 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8515 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 856 5.05 %RANDOM
Rwork0.1866 16085 --
obs0.1892 16941 99.96 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.172 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 93.56 Å2 / Biso mean: 28.1218 Å2 / Biso min: 7.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.8669 Å2-0 Å20 Å2
2--0.8669 Å2-0 Å2
3----1.7339 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 0 120 2681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082638
X-RAY DIFFRACTIONf_angle_d1.0033556
X-RAY DIFFRACTIONf_chiral_restr0.071386
X-RAY DIFFRACTIONf_plane_restr0.004435
X-RAY DIFFRACTIONf_dihedral_angle_d15.844990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7004-2.86950.23031400.200226072747
2.8695-3.09090.3261460.213226222768
3.0909-3.40170.26141500.217226262776
3.4017-3.89340.22381450.174626552800
3.8934-4.90290.18661410.149227082849
4.9029-34.11270.24491340.198628673001

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