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- PDB-1c6v: SIV INTEGRASE (CATALYTIC DOMAIN + DNA BIDING DOMAIN COMPRISING RE... -

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Basic information

Entry
Database: PDB / ID: 1c6v
TitleSIV INTEGRASE (CATALYTIC DOMAIN + DNA BIDING DOMAIN COMPRISING RESIDUES 50-293) MUTANT WITH PHE 185 REPLACED BY HIS (F185H)
Components
  • PROTEIN (SIU89134)
  • PROTEIN (SIV INTEGRASE)
KeywordsDNA BINDING PROTEIN / DNA INTEGRATION
Function / homology
Function and homology information


RNA stem-loop binding / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...RNA stem-loop binding / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / 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 / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / 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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / Retropepsin-like catalytic domain / 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 / 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 / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesSimian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChen, Z. / Yan, Y. / Munshi, S. / Li, Y. / Zruygay-Murphy, J. / Xu, B. / Witmer, M. / Felock, P. / Wolfe, A. / Sardana, V. ...Chen, Z. / Yan, Y. / Munshi, S. / Li, Y. / Zruygay-Murphy, J. / Xu, B. / Witmer, M. / Felock, P. / Wolfe, A. / Sardana, V. / Emini, E.A. / Hazuda, D. / Kuo, L.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: X-ray structure of simian immunodeficiency virus integrase containing the core and C-terminal domain (residues 50-293)--an initial glance of the viral DNA binding platform.
Authors: Chen, Z. / Yan, Y. / Munshi, S. / Li, Y. / Zugay-Murphy, J. / Xu, B. / Witmer, M. / Felock, P. / Wolfe, A. / Sardana, V. / Emini, E.A. / Hazuda, D. / Kuo, L.C.
History
DepositionDec 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Aug 9, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SIV INTEGRASE)
B: PROTEIN (SIV INTEGRASE)
C: PROTEIN (SIV INTEGRASE)
D: PROTEIN (SIV INTEGRASE)
X: PROTEIN (SIU89134)


Theoretical massNumber of molelcules
Total (without water)82,8095
Polymers82,8095
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.57, 100.00, 150.50
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHERE ARE FOUR CORE DOMAINS AND ONE DNA BINDING DOMAIN IN THE ASYMMETRIC UNIT. THE FOUR CORE DOMAINS ARE LABELLED A A, B, C AND D. THE DNA BINDING DOMAIN ARE LABELLED AS X. THE MISSING RESIDUES ARE: CORE DOMAIN A, A50-A54, A141-A151 CORE DOMAIN B; B50-B54, B141-B151, B208-B212. CORE DOMAIN C; C50-C54, C141-C150, C208-C212. CORE DOMAIN D; D50-D54, D141-D151, C208-C212. DNA BINDING DOMAIN; X214-X215 ,X230-232, X271-X292.

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Components

#1: Protein
PROTEIN (SIV INTEGRASE)


Mass: 18405.967 Da / Num. of mol.: 4 / Fragment: RESIDUES 813-976 / Mutation: F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): BL2 / Variant (production host): DE3 / References: UniProt: Q88016
#2: Protein PROTEIN (SIU89134)


Mass: 9185.444 Da / Num. of mol.: 1 / Fragment: RESIDUES 979-1059
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): BL2 / Variant (production host): DE3 / References: UniProt: Q87706, UniProt: Q88016*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.7 / Details: 0.1 M MES, PH=5.7, PEG6K 8%, 15% DIOXANE
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMes11
28 %(v/v)PEG600011
31.5 %(v/v)dioxane11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9817
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9817 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 22129 / % possible obs: 92.5 % / Observed criterion σ(I): 3 / Redundancy: 13.9 % / Rmerge(I) obs: 0.113
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 1.5 / % possible all: 66.8
Reflection
*PLUS
Num. measured all: 309679
Reflection shell
*PLUS
% possible obs: 66.8 %

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Processing

Software
NameClassification
CCP4model building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: SIR, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ITG AND 1IHV

1itg

1ihv


Resolution: 3→6 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.362 599 10 %RANDOM
Rwork0.203 ---
obs0.203 15576 --
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 0 66 5030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 3→3.12 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.473 55
Rwork0.239 599

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