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- PDB-1asw: AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED ... -

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Basic information

Entry
Database: PDB / ID: 1asw
TitleAVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, HEPES PH 7.5 USING SELENOMETHIONINE SUBSTITUTED PROTEIN; DATA COLLECTED AT-165 DEGREES C
ComponentsAVIAN SARCOMA VIRUS INTEGRASE
KeywordsDNA INTEGRATION
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
ISOPROPYL ALCOHOL / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesAvian sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsBujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: High-resolution structure of the catalytic domain of avian sarcoma virus integrase.
Authors: Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Katz, R.A. / Skalka, A.M.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Expression, Purification, and Crystallization of Natural and Selenomethionyl Recombinant Ribonuclease H from Escherichia Coli
Authors: Yang, W. / Hendrickson, W.A. / Kalman, E.T. / Crouch, R.J.
History
DepositionAug 25, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AVIAN SARCOMA VIRUS INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3813
Polymers18,0831
Non-polymers2982
Water3,369187
1
A: AVIAN SARCOMA VIRUS INTEGRASE
hetero molecules

A: AVIAN SARCOMA VIRUS INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7636
Polymers36,1662
Non-polymers5974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Unit cell
Length a, b, c (Å)65.400, 65.400, 80.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 73

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Components

#1: Protein AVIAN SARCOMA VIRUS INTEGRASE


Mass: 18083.082 Da / Num. of mol.: 1
Mutation: INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209)
Source method: isolated from a genetically manipulated source
Details: CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, HEPES PH 7.5 USING SELENOMETHIONINE-SUBSTITUTED PROTEIN, DATA COLLECTED AT LOW TEMPERATURE
Source: (gene. exp.) Avian sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT-RUPPIN B / Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, UniProt: O92956*PLUS
#2: 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
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Source detailsORIGINAL VIRAL DNA CLONE: JU ET AL., J. VIROL. 33:1026-1033 (1980) ORIGINAL EXPRESSION CLONE: TERRY ...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 CLONE FOR CORE: KULKOSKY ET AL., J. VIROL. 206:448-456 (1995)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG40001reservoir
210 %isopropanol1reservoir
3100 mMHEPES1reservoir
46-7.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9464, 0.9792, 0.9790
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 10, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94641
20.97921
30.9791
ReflectionResolution: 1.8→25 Å / Num. obs: 12157 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 7.07 % / Rmerge(I) obs: 0.068
Reflection
*PLUS
Rmerge(I) obs: 0.068

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.208 --
obs0.139 10188 72.3 %
Displacement parametersBiso mean: 18.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 15 191 1389
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.017
X-RAY DIFFRACTIONp_angle_d0.0470.043
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.058
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2992.5
X-RAY DIFFRACTIONp_mcangle_it3.3883.5
X-RAY DIFFRACTIONp_scbond_it4.6894
X-RAY DIFFRACTIONp_scangle_it6.2717
X-RAY DIFFRACTIONp_plane_restr0.0160.022
X-RAY DIFFRACTIONp_chiral_restr0.1680.18
X-RAY DIFFRACTIONp_singtor_nbd0.2050.5
X-RAY DIFFRACTIONp_multtor_nbd0.2290.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2250.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63.6
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor38.612
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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