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- PDB-3uxu: The structure of the catalytic domain of the Sulfolobus Spindle-s... -

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Basic information

Entry
Database: PDB / ID: 3uxu
TitleThe structure of the catalytic domain of the Sulfolobus Spindle-shaped viral integrase reveals an evolutionarily conserved catalytic core and supports a mechanism of DNA cleavage in trans
ComponentsProbable integrase
KeywordsRECOMBINATION / SSV1 / Archaea / Archaeal virus / hyperthermophilic / Integrase / Disulfide
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
PHOSPHATE ION / Integrase
Similarity search - Component
Biological speciesSulfolobus virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.706 Å
AuthorsEilers, B.J. / Young, M.J. / Lawrence, C.M.
CitationJournal: J.Virol. / Year: 2012
Title: The Structure of an Archaeal Viral Integrase Reveals an Evolutionarily Conserved Catalytic Core yet Supports a Mechanism of DNA Cleavage in trans.
Authors: Eilers, B.J. / Young, M.J. / Lawrence, C.M.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1162
Polymers20,0211
Non-polymers951
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.963, 73.963, 176.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Probable integrase


Mass: 20021.246 Da / Num. of mol.: 1 / Fragment: catalytic domain (176-334) / Mutation: V215I, T307A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus virus 1 / Strain: Sulfolobus solfataricus / Gene: d335 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P20214
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 1% Tryptone, and 0.1 M HEPES at pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.84917
SYNCHROTRONSSRL BL11-120.97891, 0.91837, 0.97939
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELDec 5, 2009Rh coated flat mirror
DECTRIS PILATUS 6M2PIXELDec 5, 2009Rh coated flat mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degsSINGLE WAVELENGTHMx-ray1
2Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degsMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.849171
20.978911
30.918371
40.979391
ReflectionResolution: 2.7→50 Å / Num. obs: 8414 / % possible obs: 99.9 % / Observed criterion σ(F): 10.2 / Observed criterion σ(I): 595.3 / Redundancy: 13.5 % / Rmerge(I) obs: 0.033 / Rsym value: 0.043 / Net I/σ(I): 5.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 42.3 / Rsym value: 0.315 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
AutoSolphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.706→36.32 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / SU B: 19.855 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21442 410 4.9 %RANDOM
Rwork0.19286 ---
obs0.19394 7900 99.14 %-
all-8310 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.971 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.41 Å20 Å2
2--0.81 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.706→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 5 17 1351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221386
X-RAY DIFFRACTIONr_bond_other_d0.0050.02998
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9661874
X-RAY DIFFRACTIONr_angle_other_deg0.86832407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4295162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.38421.87564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33715257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7981513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021491
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9641.5799
X-RAY DIFFRACTIONr_mcbond_other0.1141.5320
X-RAY DIFFRACTIONr_mcangle_it3.53621300
X-RAY DIFFRACTIONr_scbond_it3.6973587
X-RAY DIFFRACTIONr_scangle_it6.4724.5572
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.706→2.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 31 -
Rwork0.268 550 -
obs--95.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4759-1.4461.63172.1833-2.1613.98990.20370.0957-0.2393-0.1593-0.24620.05630.40640.13020.04250.22630.0016-0.0660.26370.070.237418.258717.06181.2491
27.0582-0.941.40883.9663-1.37996.145-0.0774-0.3195-0.12070.17950.39080.3498-0.1058-0.4316-0.31340.116-0.00950.0220.3450.13850.21451.879722.65496.453
35.1766-12.84944.006532.0989-9.89853.117-0.2514-0.06550.27070.14440.0958-0.6992-0.2307-0.0050.15570.5419-0.1304-0.06330.5332-0.00750.2803-0.212234.50885.1862
44.2847-0.56212.23090.1633-0.76214.126-0.2594-0.4903-0.06460.05710.09710.0397-0.3019-0.17270.16230.3068-0.0231-0.07840.25320.10970.285612.882518.78310.1428
56.81850.02076.26673.4335-2.57387.72410.07410.40950.03250.0894-0.302-0.2211-0.04510.59780.22790.1815-0.019-0.02670.40220.02770.203320.179123.5081-1.1197
66.1199-2.8777-3.35251.64850.65184.78610.13960.13150.20130.0069-0.0751-0.0708-0.29570.0759-0.06440.2186-0.0071-0.09130.25950.07410.28682.011433.2072-5.3289
76.8785-4.64510.03956.78260.5232.20050.20910.0675-0.4096-0.2102-0.16440.42260.1022-0.0853-0.04470.1751-0.0042-0.12220.27670.03750.25650.709323.0852-7.9168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A176 - 210
2X-RAY DIFFRACTION2A211 - 238
3X-RAY DIFFRACTION3A239 - 248
4X-RAY DIFFRACTION4A249 - 268
5X-RAY DIFFRACTION5A269 - 290
6X-RAY DIFFRACTION6A291 - 312
7X-RAY DIFFRACTION7A313 - 334

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