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- PDB-1c1a: CRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE -

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Basic information

Entry
Database: PDB / ID: 1c1a
TitleCRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE
ComponentsRSV INTEGRASE
KeywordsVIRAL PROTEIN / INTEGRASE / ROUS SARCOMA VIRUS / HIV / VIRUS/VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 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 ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / 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
Integrase, C-terminal domain superfamily, retroviral / 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, C-terminal domain superfamily, retroviral / 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. / SH3 type barrels. / 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 / 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
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING / Resolution: 3.1 Å
AuthorsYang, Z.-N. / Mueser, T.C. / Bushman, F.D. / Hyde, C.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase.
Authors: Yang, Z.N. / Mueser, T.C. / Bushman, F.D. / Hyde, C.C.
History
DepositionJul 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Other
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RSV INTEGRASE
B: RSV INTEGRASE


Theoretical massNumber of molelcules
Total (without water)53,1992
Polymers53,1992
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-26 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.240, 46.339, 94.309
Angle α, β, γ (deg.)90.00, 101.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein RSV INTEGRASE


Mass: 26599.531 Da / Num. of mol.: 2 / Fragment: RESIDUES 49-286 / Mutation: F199K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, RNA-directed DNA polymerase

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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: 2.66 Å3/Da / Density % sol: 41.7 %
Description: THE CATALYTIC DOMAIN WAS POSITIONED BY MOLECULAR REPLACEMENT USING AMORE WITH 1VSE AS STARTING MODEL. MAD PHASED MAP WAS CACULATED USING THE SAME ORIGIN AS THE MOLECULAR REPLACEMENT ...Description: THE CATALYTIC DOMAIN WAS POSITIONED BY MOLECULAR REPLACEMENT USING AMORE WITH 1VSE AS STARTING MODEL. MAD PHASED MAP WAS CACULATED USING THE SAME ORIGIN AS THE MOLECULAR REPLACEMENT SOLUTION AND SE POSITIONS WERE CONFIRMED. THE SH3- FOLD OF C-DOMAIN WAS LOCATED VISUALLY IN THE MAD MAP, HIV C-DOMAIN (1IHV) MONOMER WAS POSITIONED MANUALLY IN THE MAP AND MODIFIED TO RSV SEQUENCES DURING MODEL BUILDING.
Crystal growDetails: ROD-SHAPED CRYSTALS WERE GROWN BY SITTING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.1M SODIUM CACODYLATE, 0.02M IMIDAZOLE, PH 7.2, 10% PEG3350, AND ...Details: ROD-SHAPED CRYSTALS WERE GROWN BY SITTING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.1M SODIUM CACODYLATE, 0.02M IMIDAZOLE, PH 7.2, 10% PEG3350, AND 20% (V/V) ETHYLENE GLYCOL. THE DROP CONTAINED 1:1 MIXTURE OF RESERVOIR SOLUTION AND PROTEIN (10-15 MG/ML)
Crystal grow
*PLUS
Temperature: 0-5 unknown / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 M1reservoirKCl
20.01 M1reservoirMgCl2
30.05 Msodium cacodylate1reservoir
410 %(w/v)PEG33501reservoir
525 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 1998
RadiationProtocol: MULTIPLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 11250 / % possible obs: 98.6 % / Observed criterion σ(I): 0.04 / Redundancy: 3.4 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5.5 / % possible all: 96.5
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD PHASING
Starting model: ASV INTEGRASE CATALYTIC DOMAIN (1VSE)

1vse


Resolution: 3.1→15 Å / Cross valid method: THROUGHOUT / σ(F): 0.2 / Stereochemistry target values: ENGH & HUBER
Details: THIS IS ONE OF SE-MET DATA SET COLLECTTED FOR MAD PHASING ALTHOUGH SE ATOMS WERE NOT MODELED. CAUTION SHOULD BE TAKEN IN INTERPRETING THOSE RESIDUES WITH B FACTORS IN UPPER 60S OR HIGHER
RfactorNum. reflection% reflectionSelection details
Rfree0.337 525 5.2 %RANDOM
Rwork0.256 ---
obs0.256 10183 5.1 %-
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-0.817 Å20 Å2-10.779 Å2
2---3.077 Å20 Å2
3---2.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 0 0 3397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev position (Å)Weight position
11X-RAY DIFFRACTION0.062200
22X-RAY DIFFRACTION0.097150
LS refinement shellResolution: 3.1→3.21 Å
RfactorNum. reflection% reflection
Rfree0.459 42 4.15 %
Rwork0.334 977 -
obs--96.5 %
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97

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