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- PDB-4dks: A spindle-shaped virus protein (chymotrypsin treated) -

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Basic information

Entry
Database: PDB / ID: 4dks
TitleA spindle-shaped virus protein (chymotrypsin treated)
ComponentsProbable integrase
KeywordsRECOMBINATION / Catalytic domain / Integrase / The C174 domain of SSV1 Int / seven-helices / three-stranded antiparallel-sheet'
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity / symbiont entry into host cell / DNA binding
Similarity search - Function
ORF D-335-like / Integrase SSV1, C-terminal / ORF D-335-like protein / Archaeal phage integrase / Intergrase catalytic core / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Integrase, catalytic domain ...ORF D-335-like / Integrase SSV1, C-terminal / ORF D-335-like protein / Archaeal phage integrase / Intergrase catalytic core / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Integrase, catalytic domain / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSulfolobus virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOuyang, S. / Liang, W. / Huang, L. / Liu, Z.-J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase.
Authors: Zhan, Z. / Ouyang, S. / Liang, W. / Zhang, Z. / Liu, Z.J. / Huang, L.
History
DepositionFeb 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable integrase


Theoretical massNumber of molelcules
Total (without water)19,1221
Polymers19,1221
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.224, 75.224, 96.091
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-443-

HOH

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Components

#1: Protein Probable integrase


Mass: 19122.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus virus 1 / Gene: d335 / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20214
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FULL SEQUENCE WHICH WAS PREPARED FOR THE CRYSTLLIZATION IS AS FOLLOWS. ...THE FULL SEQUENCE WHICH WAS PREPARED FOR THE CRYSTLLIZATION IS AS FOLLOWS. MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGS MTKDKTRYKYGDYILRERKGRYYVYKLEYENGEVKERYVGPLADVVESYL KMKLGVVGDTPLQADPPGFEPGTSGSGGGKEGTERRKIALVANLRQYATD GNIKAFYDYLMNERGISEKTAKDYINAISKPYKETRDAQKAYRLFARFLA SRNIIHDEFADKILKAVKVKKANADIYIPTLEEIKRTLQLAKDYSENVYF IYRIALESGVRLSEILKVLKEPERDICGNDVCYYPLSWTRGYKGVFYVFH ITPLKRVEVTKWAIADFERRHKDAIAIKYFRKFVASKMAELSVPLDIIDF IQGRKPTRVLTQHYVSLFGIAKEQYKKYAEWLKGV HOWEVER, THE PROTEIN WAS CRYSTALLIZED BY IN SITU PROTEOLYSIS METHODS (CHYMOTRYPSIN TREATED). THE N-TERMINAL AND SOME LOOPS MISSED IN THE STRUCTURE.

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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: 3.55 Å3/Da / Density % sol: 65.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaCl or MgCl2, 0.1M HEPES, 25%(w/v) polyethylene glycol 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8010 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 56.1 Å2
Reflection shellHighest resolution: 2.7 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.491 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8452 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 21.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 378 4.72 %RANDOM
Rwork0.2026 7632 --
obs0.2051 8010 99.75 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.016 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 108.29 Å2 / Biso mean: 54.3656 Å2 / Biso min: 29.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.0839 Å2-0 Å20 Å2
2---1.0839 Å2-0 Å2
3---2.1678 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 0 67 1266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091226
X-RAY DIFFRACTIONf_angle_d1.0721648
X-RAY DIFFRACTIONf_chiral_restr0.073181
X-RAY DIFFRACTIONf_plane_restr0.006202
X-RAY DIFFRACTIONf_dihedral_angle_d15.769459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-3.09060.27631290.228924592588
3.0906-3.89340.27391320.183625022634
3.8934-40.49580.24861170.205926712788

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