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- PDB-1czb: ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM HEPES -

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Basic information

Entry
Database: PDB / ID: 1czb
TitleATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM HEPES
ComponentsAVIAN SARCOMA VIRUS INTEGRASE
KeywordsTRANSFERASE / MIXED BETA-SHEET SURROUNDED BY ALPHA-HELICES
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / RNA 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 / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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 speciesAvian sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.06 Å
AuthorsLubkowski, J. / Dauter, Z. / Yang, F. / Alexandratos, J. / Merkel, G. / Skalka, A.M. / Wlodawer, A.
CitationJournal: Biochemistry / Year: 1999
Title: Atomic resolution structures of the core domain of avian sarcoma virus integrase and its D64N mutant.
Authors: Lubkowski, J. / Dauter, Z. / Yang, F. / Alexandratos, J. / Merkel, G. / Skalka, A.M. / Wlodawer, A.
History
DepositionSep 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,0942
Polymers17,8551
Non-polymers2381
Water2,468137
1
A: AVIAN SARCOMA VIRUS INTEGRASE
hetero molecules

A: AVIAN SARCOMA VIRUS INTEGRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1874
Polymers35,7112
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)65.370, 65.370, 80.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is (at least) a dimer constructed from chain A and a symmetry partner generated by the two-fold symmetry operator.

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Components

#1: Protein AVIAN SARCOMA VIRUS INTEGRASE


Mass: 17855.441 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN / Mutation: INS(P48, L49, R50, E51, N208, L209)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian sarcoma virus / Genus: Alpharetrovirus / 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 / HEPES


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


Mass: 18.015 Da / Num. of mol.: 137 / 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 & 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 10% ISOPROPANOL, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Bujacz, G., (1995) J. Mol. Biol., 253, 333.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1reservoir
210 %isopropanol1reservoir
36-7.5 mg/mlprotein1drop
420 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.06→15 Å / Num. all: 69419 / Num. obs: 69419 / % possible obs: 90.01 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 32.3
Reflection shellResolution: 1.06→1.08 Å / Redundancy: 4.2 % / Num. unique all: 2467 / % possible all: 86.7
Reflection
*PLUS
Num. measured all: 250390
Reflection shell
*PLUS
% possible obs: 86.7 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
X-PLORmodel building
SHELXLrefinement
MAR345data collection
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.06→10 Å / Num. parameters: 1157 / Num. restraintsaints: 1443 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1639 1490 -random
Rwork0.1433 ---
all0.143 74543 --
obs0.143 74543 94.4 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 1001 / Occupancy sum non hydrogen: 1189
Refinement stepCycle: LAST / Resolution: 1.06→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1131 0 15 137 1283
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0.024
X-RAY DIFFRACTIONs_from_restr_planes0.347
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.068
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.347

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