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- PDB-3o4q: Crystal structure of the Rous Associated Virus Integrase catalyti... -

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Basic information

Entry
Database: PDB / ID: 3o4q
TitleCrystal structure of the Rous Associated Virus Integrase catalytic domain A182T in citrate buffer pH 6.2
Componentsintegrase
KeywordsDNA BINDING PROTEIN / DNA integration process
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 / DNA recombination / Hydrolases; Acting on ester bonds / nucleic acid binding / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / 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 / 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
CITRATE ANION / Gag-Pol polyprotein / Pol protein
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsBallandras, A. / Robert, X. / Gouet, P.
CitationJournal: Plos One / Year: 2011
Title: A crystal structure of the catalytic core domain of an avian sarcoma and leukemia virus integrase suggests an alternate dimeric assembly.
Authors: Ballandras, A. / Moreau, K. / Robert, X. / Confort, M.P. / Merceron, R. / Haser, R. / Ronfort, C. / Gouet, P.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5912
Polymers16,4021
Non-polymers1891
Water2,198122
1
A: integrase
hetero molecules

A: integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1824
Polymers32,8042
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2040 Å2
ΔGint-8 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.490, 65.490, 79.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein integrase /


Mass: 16401.818 Da / Num. of mol.: 1 / Fragment: INRAV1 CCD, residues 625-771 / Mutation: A182T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Gene: pol / Plasmid: pETG10a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q4ZJZ6, UniProt: O92956*PLUS
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% (w/v) PEG 4000, 10% isopropanol and 0.1 M Na citrate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97968 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2010 / Details: Synchrotron optics
RadiationMonochromator: Synchrotron beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97968 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. all: 24970 / Num. obs: 25642 / % possible obs: 97.38 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.049 / Net I/σ(I): 20.94
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5.36 / Num. unique all: 2278 / Rsym value: 0.256 / % possible all: 95.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→19.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.276 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21125 1249 5 %RANDOM
Rwork0.16411 ---
all0.16646 23721 --
obs0.16646 23721 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.176 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 13 122 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211114
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9461511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12421.81844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40115189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5451511
X-RAY DIFFRACTIONr_chiral_restr0.1320.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021824
X-RAY DIFFRACTIONr_mcbond_it2.4431.5689
X-RAY DIFFRACTIONr_mcangle_it3.57421109
X-RAY DIFFRACTIONr_scbond_it5.7273425
X-RAY DIFFRACTIONr_scangle_it8.0694.5402
X-RAY DIFFRACTIONr_rigid_bond_restr2.86431114
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 87 -
Rwork0.197 1655 -
obs--100 %

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