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- PDB-1vsk: ASV INTEGRASE CORE DOMAIN D64N MUTATION IN CITRATE BUFFER PH 6.0 -

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Basic information

Entry
Database: PDB / ID: 1vsk
TitleASV INTEGRASE CORE DOMAIN D64N MUTATION IN CITRATE BUFFER PH 6.0
ComponentsINTEGRASE
KeywordsHYDROLASE / ENDONUCLEASE / TRANSFERASE
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / virion component / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain ...Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesRous sarcoma virus - Schmidt-Ruppin B
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsLubkowski, J. / Yang, F. / Alexandratos, J. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Structural basis for inactivating mutations and pH-dependent activity of avian sarcoma virus integrase.
Authors: Lubkowski, J. / Yang, F. / Alexandratos, J. / Merkel, G. / Katz, R.A. / Gravuer, K. / Skalka, A.M. / Wlodawer, A.
History
DepositionSep 18, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)15,9981
Polymers15,9981
Non-polymers00
Water1,910106
1
A: INTEGRASE

A: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)31,9972
Polymers31,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)67.159, 67.159, 79.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE BIOLOGICAL UNIT IS NOT YET KNOWN. THE MINIMUM MULTIMER IS BELIEVED TO CONTAIN AT LEAST THIS DIMER, SHOWN IN BOTH HIV-1 AND ASV INTEGRASE CORE DOMAIN STRUCTURES.

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Components

#1: Protein INTEGRASE


Mass: 15998.403 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN / Mutation: D64N
Source method: isolated from a genetically manipulated source
Details: P03354 FRAGMENT OF POLYPROTEIN POL-RSVP / Source: (gene. exp.) Rous sarcoma virus - Schmidt-Ruppin B / Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: SCHMIDT-RUPPIN B / Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli)
References: UniProt: P03354, UniProt: O92956*PLUS, RNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE "POL_RSVP" SEQUENCE IS A ...THE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE "POL_RSVP" SEQUENCE IS A RESULT OF VIRAL STRAIN VARIATION. THE STRAIN USED FOR THIS WORK, ROUS SARCOMA VIRUS SCHMIDT-RUPPIN B, COMPARED TO "POL-RSVP" SEQUENCE DIFFERS AT TWO POSITIONS WITH THE CONSERVATIVE AMINO ACID RESIDUE DIFFERENCES NOTED (VAL->ALA 101 AND ARG-> LYS 166). MUTATION D64N ENGINEERED FOR THIS STUDY. ALA 101, VIRAL STRAIN DIFFERENCES LYS 166, VIRAL STRAIN DIFFERENCES ASN 64, ENGINEERED MUTATION FOR THIS STUDY

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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: 2.52 Å3/Da / Density % sol: 38 %
Crystal growpH: 5.6
Details: 20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.6
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Bujacz, G., (1995) J. Mol. Biol., 253, 333.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-7.5 mg/mlprotein1drop
2100 mMHEPES1reservoir
310 %isopropanol1reservoir
420 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Oct 31, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 10132 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rsym value: 0.077 / Net I/σ(I): 20.7
Reflection shellResolution: 2.15→2.21 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.415 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 85055 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.415

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementStarting model: PDB ENTRY 1ASV

1asv


Resolution: 2.2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
Details: ATOMIC OCCUPANCIES OF DISORDERED ATOMS ARE SET TO ZERO IN COORDINATES
RfactorNum. reflection% reflectionSelection details
Rfree0.249 841 10 %RANDOM
Rwork0.159 ---
obs0.159 8372 88.1 %-
Displacement parametersBiso mean: 34.8 Å2
Refine analyzeLuzzati d res low obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 0 106 1337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.256 105 8.94 %
Rwork0.221 812 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_FY.PROTOPHCSDX_FY.PRO
X-RAY DIFFRACTION2PARAM19.SOLVTOPH19.SOLV
X-RAY DIFFRACTION3
X-RAY DIFFRACTION4
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.28
LS refinement shell
*PLUS
Rfactor obs: 0.221

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