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- PDB-1vsm: ASV INTEGRASE CORE DOMAIN IN CITRATE BUFFER PH 5.0 -

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Basic information

Entry
Database: PDB / ID: 1vsm
TitleASV INTEGRASE CORE DOMAIN IN CITRATE BUFFER PH 5.0
ComponentsPROTEIN (INTEGRASE)
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
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PROTEIN (INTEGRASE)


Theoretical massNumber of molelcules
Total (without water)15,9991
Polymers15,9991
Non-polymers00
Water2,252125
1
A: PROTEIN (INTEGRASE)

A: PROTEIN (INTEGRASE)


Theoretical massNumber of molelcules
Total (without water)31,9992
Polymers31,9992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)67.091, 67.091, 79.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (INTEGRASE)


Mass: 15999.388 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin)
Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: Schmidt-Ruppin / 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.: 125 / 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->ALA101 & ARG-> LYS 166).

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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 5.0, 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: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 9, 1998 / Details: MIRRORS
RadiationMonochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 9166 / % possible obs: 85.7 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rsym value: 0.08 / Net I/σ(I): 3
Reflection shellResolution: 2.13→2.19 Å / Mean I/σ(I) obs: 10 / Rsym value: 0.312 / % possible all: 86.5
Reflection
*PLUS
Num. measured all: 28268 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 86.5 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ASV

1asv


Resolution: 2.15→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.238 667 10 %RANDOM
Rwork0.146 ---
obs0.146 7569 74.9 %-
Displacement parametersBiso mean: 32 Å2
Refine analyzeLuzzati d res low obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 0 125 1250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.35
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: 2.15→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.234 66 5.3 %
Rwork0.219 704 -
obs--62.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_FY.PROTOPHCSDX_FY.PRO
X-RAY DIFFRACTION2PARAM19.SOLVTOPH19.SOLV
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.35
LS refinement shell
*PLUS
Rfactor Rfree: 0.234 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.219

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