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- PDB-2x74: Human foamy virus integrase - catalytic core. -

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Basic information

Entry
Database: PDB / ID: 2x74
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 / SAD / Resolution: 2.34 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 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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
D: INTEGRASE
E: INTEGRASE
F: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)136,5926
Polymers136,5926
Non-polymers00
Water3,387188
1
C: INTEGRASE
D: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)45,5312
Polymers45,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-11.9 kcal/mol
Surface area16280 Å2
MethodPISA
2
A: INTEGRASE
B: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)45,5312
Polymers45,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-10.3 kcal/mol
Surface area17390 Å2
MethodPISA
3
E: INTEGRASE
F: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)45,5312
Polymers45,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-6.2 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.180, 89.110, 177.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
INTEGRASE / IN / P42IN


Mass: 22765.379 Da / Num. of mol.: 6 / Fragment: CATALYTIC CORE, RESIDUES 861-1060 / Mutation: YES
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.: 188 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 878 TO MSE ENGINEERED RESIDUE IN CHAIN A, ILE 978 TO MSE ...ENGINEERED RESIDUE IN CHAIN A, ILE 878 TO MSE ENGINEERED RESIDUE IN CHAIN A, ILE 978 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU1004 TO MSE ENGINEERED RESIDUE IN CHAIN B, ILE 878 TO MSE ENGINEERED RESIDUE IN CHAIN B, ILE 978 TO MSE ENGINEERED RESIDUE IN CHAIN B, LEU1004 TO MSE ENGINEERED RESIDUE IN CHAIN C, ILE 878 TO MSE ENGINEERED RESIDUE IN CHAIN C, ILE 978 TO MSE ENGINEERED RESIDUE IN CHAIN C, LEU1004 TO MSE ENGINEERED RESIDUE IN CHAIN D, ILE 878 TO MSE ENGINEERED RESIDUE IN CHAIN D, ILE 978 TO MSE ENGINEERED RESIDUE IN CHAIN D, LEU1004 TO MSE ENGINEERED RESIDUE IN CHAIN E, ILE 878 TO MSE ENGINEERED RESIDUE IN CHAIN E, ILE 978 TO MSE ENGINEERED RESIDUE IN CHAIN E, LEU1004 TO MSE ENGINEERED RESIDUE IN CHAIN F, ILE 878 TO MSE ENGINEERED RESIDUE IN CHAIN F, ILE 978 TO MSE ENGINEERED RESIDUE IN CHAIN F, LEU1004 TO MSE
Has protein modificationY
Sequence detailsR180K IN CDNA, I127M, I227M, L253M FOR PHASING WITH SEMET

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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: 2.66 Å3/Da / Density % sol: 40.8 % / Description: THIS DATA SET WAS USED FOR REFINEMENT
Crystal growDetails: 1.8-2M AMMONIUM FORMATE, 100MM HEPES PH 7.5, 10-15% GLYCEROL

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.033, 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 12, 2008 / Details: KB-MIRRORS
RadiationMonochromator: SI (111) CHANNEL-CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
20.9791
ReflectionResolution: 2.34→34.58 Å / Num. obs: 57496 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 51.072 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.1
Reflection shellResolution: 2.34→2.46 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.34→34.58 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.57 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29391 2843 5 %RANDOM
Rwork0.23329 ---
obs0.23633 54583 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.34→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8792 0 0 188 8980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229130
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.97312433
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86251082
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22623.518398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.382151543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.881552
X-RAY DIFFRACTIONr_chiral_restr0.0810.21397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226866
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_it1.2492.55498
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1373.59014
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23543632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0785.53419
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: 2.337→2.397 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 186 -
Rwork0.322 3736 -
obs--92.61 %

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