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- PDB-2x78: Human foamy virus integrase - catalytic core. -

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Basic information

Entry
Database: PDB / ID: 2x78
TitleHuman foamy virus integrase - catalytic core.
ComponentsINTEGRASE
KeywordsVIRAL PROTEIN / RETROVIRAL INTEGRASE / DNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / DNA INTEGRATION / ASPARTYL PROTEASE / DNA RECOMBINATION / TRANSFERASE / NUCLEASE / HYDROLASE
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding
Similarity search - Function
Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase ...Spumavirus aspartic protease A9 / Retroviral integrase, C-terminal SH3 domain / Spumavirus aspartic protease (A9) / Retroviral integrase C-terminal SH3 domain / Foamy virus protease (FV PR) domain profile. / : / Integrase zinc-binding domain / Integrase zinc binding domain / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHUMAN SPUMARETROVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRety, S. / Delelis, O. / Rezabkova, L. / Dubanchet, B. / Legrand, P. / Silhan, J. / Lewit-Bentley, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structural Studies of the Catalytic Core of the Primate Foamy Virus (Pfv-1) Integrase
Authors: Rety, S. / Rezabkova, L. / Dubanchet, B. / Silhan, J. / Legrand, P. / Lewit-Bentley, A.
History
DepositionFeb 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Other ...Database references / Other / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRASE
B: INTEGRASE
C: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)67,5713
Polymers67,5713
Non-polymers00
Water6,521362
1
A: INTEGRASE
B: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)45,0472
Polymers45,0472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-10.5 kcal/mol
Surface area16030 Å2
MethodPISA
2
C: INTEGRASE

C: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)45,0472
Polymers45,0472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3720 Å2
ΔGint-15.3 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.800, 98.040, 240.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein INTEGRASE / IN / P42IN / PFV INTEGRASE


Mass: 22523.686 Da / Num. of mol.: 3 / Fragment: CATALYTIC CORE, RESIDUES 861-1060
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN SPUMARETROVIRUS / Strain: HSRV2 / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14350
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DIFFERENCE R71K (WHICH IS R180K IN THE NEW NUMBERING) IS DUE TO A DIFFERENCE IN THE PFV-POL ...THE DIFFERENCE R71K (WHICH IS R180K IN THE NEW NUMBERING) IS DUE TO A DIFFERENCE IN THE PFV-POL CDNA SEQUENCE THAT WAS USED TO CLONE THE CATALYTIC CORE.R180K MUTATION IN CDNA

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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: 33.8 % / Description: NONE
Crystal growDetails: 100 MM SODIUM CITRATE, PH=5, 14% PEG 8000, 10% GLUCOSE, 5% MPD, 4MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2007 / Details: MIRRORS
RadiationMonochromator: SI (111) CHANNEL-CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→49.02 Å / Num. obs: 38236 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 26.586 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 53.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X74

2x74


Resolution: 2→49.02 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.66 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27208 1910 5 %RANDOM
Rwork0.21187 ---
obs0.21485 36271 91.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 0 362 4601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224377
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9755961
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43323.278180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39815737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8451525
X-RAY DIFFRACTIONr_chiral_restr0.0810.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213233
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2352.52659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1853.54349
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.22841718
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4725.51612
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 51 -
Rwork0.305 1073 -
obs--36.74 %

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