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- PDB-1vsi: ASV INTEGRASE CORE DOMAIN WITH CA(II) COFACTOR -

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Basic information

Entry
Database: PDB / ID: 1vsi
TitleASV INTEGRASE CORE DOMAIN WITH CA(II) COFACTOR
ComponentsINTEGRASE
KeywordsENDONUCLEASE / HYDROLASE / ENDORIBONUCLEASE / RNA-DIRECTED DNA POLYMERASE
Function / homology
Function and homology information


ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion component / DNA integration / viral genome integration into host DNA / 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 / virion component / DNA integration / viral genome integration into host DNA / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / Ribonuclease H superfamily / Aspartic peptidase domain 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 / ISOSTRUCTURAL TO PDB ENTRY 1VSF / Resolution: 2.2 Å
AuthorsBujacz, G. / Alexandratos, J. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity.
Authors: Bujacz, G. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Andrake, M. / Katz, R.A. / Skalka, A.M.
History
DepositionMar 4, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1VSF
Remark 700 SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1VSF

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0463
Polymers16,7671
Non-polymers2782
Water1,78399
1
A: INTEGRASE
hetero molecules

A: INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0916
Polymers33,5352
Non-polymers5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)66.150, 66.150, 80.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE BIOLOGICALLY ACTIVE MOLECULE IS A DIMER.

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Components

#1: Protein INTEGRASE


Mass: 16767.285 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209
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
Description: ORIGINAL VIRAL DNA CLONE\: JU ET AL., J. VIROL. 33\:1026-1033 (1980), ORIGINAL EXPRESSION CLONE TERRY ET AL., J. VIROL. 62\:2358-2365 (1988), EXPRESSION
Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, UniProt: O92956*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALA 101, VIRAL STRAIN DIFFERENCES LYS 166, VIRAL STRAIN DIFFERENCES REFERENCE: THE APPARENT ...ALA 101, VIRAL STRAIN DIFFERENCES LYS 166, VIRAL STRAIN DIFFERENCES REFERENCE: 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 THE POL-RSVP SEQUENCE DIFFERS AT TWO POSITIONS WITH THE CONSERVATIVE AMINO ACID RESIDUE DIFFERENCES VAL -> ALA 101, 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: 2.64 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM CACL2.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG40001reservoir
2100 mMHEPES1reservoir
310 %isopropanol1reservoir
46-7.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 8, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 9230 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.11 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.05 / Rsym value: 0.375 / % possible all: 92.1

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Processing

Software
NameClassification
PROFFTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: ISOSTRUCTURAL TO PDB ENTRY 1VSF
Resolution: 2.2→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.171 --
obs-8866 95.5 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 16 99 1243
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.053
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.6342.5
X-RAY DIFFRACTIONp_mcangle_it4.0943.4
X-RAY DIFFRACTIONp_scbond_it5.6733.8
X-RAY DIFFRACTIONp_scangle_it8.1016.6
X-RAY DIFFRACTIONp_plane_restr0.0180.025
X-RAY DIFFRACTIONp_chiral_restr0.1590.18
X-RAY DIFFRACTIONp_singtor_nbd0.2140.4
X-RAY DIFFRACTIONp_multtor_nbd0.220.4
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.220.4
X-RAY DIFFRACTIONp_planar_tor33.6
X-RAY DIFFRACTIONp_staggered_tor19.210
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.410
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS

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