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- PDB-3kkr: Crystal structure of catalytic core domain of BIV integrase in cr... -

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Basic information

Entry
Database: PDB / ID: 3kkr
TitleCrystal structure of catalytic core domain of BIV integrase in crystal form I
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN / beta-strands flanked by alpha-helices
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...microtubule-dependent intracellular transport of viral material towards nucleus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / 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 / host cell / viral nucleocapsid / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
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 ...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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retrovirus capsid, C-terminal / 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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesBovine immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.453 Å
AuthorsShen, Y.
CitationJournal: Protein Cell / Year: 2010
Title: Crystal structures of catalytic core domain of BIV integrase: implications for the interaction between integrase and target DNA
Authors: Yao, X. / Fang, S. / Qiao, W. / Geng, Y. / Shen, Y.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3846
Polymers17,0741
Non-polymers3105
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,76912
Polymers34,1492
Non-polymers62010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2540 Å2
ΔGint-11 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.320, 82.320, 51.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

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Components

#1: Protein Integrase / IN


Mass: 17074.330 Da / Num. of mol.: 1 / Fragment: catalytic core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine immunodeficiency virus / Strain: R29 / Gene: gag-pol / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: P19560
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, sodium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 1, 2008
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 6840 / Num. obs: 6827 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 39.63 Å2 / Rsym value: 0.046 / Net I/σ(I): 49.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 14 % / Mean I/σ(I) obs: 14.6 / Num. unique all: 665 / Rsym value: 0.225 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BIS

1bis


Resolution: 2.453→20.978 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.853 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 20.64 / Stereochemistry target values: ML / Details: The structure was refined also with CNS1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.242 327 4.85 %RANDOM
Rwork0.1916 6422 --
obs0.1938 6749 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.243 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 80.03 Å2 / Biso mean: 40.078 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.197 Å20 Å2-0 Å2
2--1.197 Å20 Å2
3----2.394 Å2
Refinement stepCycle: LAST / Resolution: 2.453→20.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 20 122 1333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061232
X-RAY DIFFRACTIONf_angle_d0.8861667
X-RAY DIFFRACTIONf_dihedral_angle_d17.701428
X-RAY DIFFRACTIONf_chiral_restr0.057188
X-RAY DIFFRACTIONf_plane_restr0.004216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4527-2.540.27841780.19963106
3.0885-20.9790.22411490.18853316

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