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- PDB-3bvp: Crystal Structure of the N-terminal Catalytic Domain of TP901-1 I... -

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Basic information

Entry
Database: PDB / ID: 3bvp
TitleCrystal Structure of the N-terminal Catalytic Domain of TP901-1 Integrase
ComponentsTP901-1 Integrase
KeywordsRECOMBINATION / DNA recombinase
Function / homology
Function and homology information


DNA strand exchange activity / DNA binding / identical protein binding
Similarity search - Function
Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Resolvase, N-terminal catalytic domain / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain ...Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Resolvase, N-terminal catalytic domain / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLactococcus phage TP901-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsYuan, P. / Van Duyne, G.D.
CitationJournal: Structure / Year: 2008
Title: Tetrameric structure of a serine integrase catalytic domain.
Authors: Yuan, P. / Gupta, K. / Van Duyne, G.D.
History
DepositionJan 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TP901-1 Integrase
B: TP901-1 Integrase


Theoretical massNumber of molelcules
Total (without water)31,5182
Polymers31,5182
Non-polymers00
Water3,603200
1
A: TP901-1 Integrase
B: TP901-1 Integrase

A: TP901-1 Integrase
B: TP901-1 Integrase


Theoretical massNumber of molelcules
Total (without water)63,0354
Polymers63,0354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.229, 67.229, 174.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: y, x, -z.

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Components

#1: Protein TP901-1 Integrase / INT


Mass: 15758.770 Da / Num. of mol.: 2 / Fragment: N-terminal catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: int / Plasmid: pGV1216 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38184
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, Mg(OAc)2, pH 6.0, vapor diffusion, hanging drop, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111.0093
SYNCHROTRONALS 8.2.120.9200, 0.9203, 0.9099
SYNCHROTRONALS 8.2.131.0722, 1.0726, 1.0540
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 8, 2007
ADSC QUANTUM 3152CCDJul 8, 2007
ADSC QUANTUM 3153CCDJul 9, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
3MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.00931
20.921
30.92031
40.90991
51.07221
61.07261
71.0541
ReflectionRedundancy: 9.4 % / Av σ(I) over netI: 11.3 / Number: 108679 / Rmerge(I) obs: 0.069 / Χ2: 1.15 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 11556 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815096.210.0311.3168.8
4.625.8197.710.0481.4878.8
4.034.6299.410.0721.6519.1
3.664.0399.810.0961.7419.4
3.43.6699.910.1051.5199.5
3.23.410010.1291.0789.6
3.043.210010.1720.8619.6
2.913.0499.910.240.6839.7
2.82.9110010.3290.6099.7
2.72.899.910.4040.6199.7
ReflectionResolution: 2.1→50 Å / Num. obs: 23563 / % possible obs: 96.4 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.056 / Χ2: 1.115 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.185.10.4418630.6571,2,377.8
2.18-2.266.10.40521350.651,2,389.7
2.26-2.377.60.35523430.6511,2,399.1
2.37-2.4990.28724080.6721,2,3100
2.49-2.659.20.19424030.7211,2,3100
2.65-2.859.20.11424130.7821,2,3100
2.85-3.149.10.0824231.1021,2,3100
3.14-3.598.90.07724591.8831,2,399.9
3.59-4.528.50.05824932.1751,2,399.4
4.52-5080.02626231.3341,2,397.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
4
5
6
Phasing MADD res high: 2.73 Å / D res low: 20 Å / FOM : 0.39 / Reflection: 9000
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1111.072212.04-19.34
1121.07268.64-21.45
1131.0549.76-9.49
1240.924.16-6.69
1250.92033.24-8.38
1260.90993.4-3.08
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Br600.9480.4710.0820.246
2Pt600.0490.4970.0420.103
Phasing MAD shell
Resolution (Å)FOM Reflection
9.19-200.67614
6.03-9.190.7926
4.78-6.030.541129
4.08-4.780.471293
3.62-4.080.371389
3.28-3.620.271392
3.03-3.280.181253
2.82-3.030.121004
Phasing MAD clust
IDExpt-ID
11
12
Phasing MAD expt
ID
1
2
Phasing dmFOM : 0.57 / FOM acentric: 0.56 / FOM centric: 0.61 / Reflection: 9187 / Reflection acentric: 7411 / Reflection centric: 1776
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-19.8920.940.960.92514299215
4.8-7.70.860.880.815341125409
3.9-4.80.780.80.7218401469371
3.4-3.90.580.580.5517521458294
2.9-3.40.320.320.3225002159341
2.7-2.90.160.160.181047901146

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.1→44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.255 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.184
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1195 5.1 %RANDOM
Rwork0.198 ---
obs0.201 23494 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--1.93 Å20 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 0 200 2332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222179
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9642938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8465267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65224.095105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29415409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9791517
X-RAY DIFFRACTIONr_chiral_restr0.090.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021606
X-RAY DIFFRACTIONr_nbd_refined0.2110.21014
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21547
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.210
X-RAY DIFFRACTIONr_mcbond_it0.91221371
X-RAY DIFFRACTIONr_mcangle_it1.47532144
X-RAY DIFFRACTIONr_scbond_it0.9492918
X-RAY DIFFRACTIONr_scangle_it1.4363792
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 69 -
Rwork0.291 1285 -
all-1354 -
obs--76.8 %
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)
15.6047-1.0724-1.17843.51-0.81158.2312-0.0797-0.3786-1.0193-0.0953-0.32580.25170.9408-0.06160.40560.20430.05190.1402-0.24650.1019-0.002664.104224.5778-2.3512
24.5524-1.5553-1.39785.06380.644211.5625-0.1674-0.0263-0.6442-0.2266-0.16650.36890.5248-0.48450.3338-0.1035-0.02470.091-0.30170.012-0.204356.398233.0371-2.6651
34.4598-3.52555.440610.4413-15.743846.7545-0.06870.1107-0.2478-0.7051-0.28910.1911.2979-0.52470.3578-0.2387-0.06390.0342-0.2976-0.0624-0.295749.500445.0614-7.8908
49.85922.1183-0.43477.5416-1.60018.1754-0.0948-0.20140.03760.0957-0.1422-0.585-0.3770.59950.237-0.1904-0.1226-0.1561-0.14640.1565-0.18766.721644.998822.1192
54.2338-0.82650.45447.0732-1.27449.0504-0.1029-0.21840.1879-0.0019-0.3521-0.8317-0.5480.75410.455-0.1871-0.1388-0.12820.03730.1681-0.212468.829545.754521.734
65.003-1.6097-0.39924.69560.29289.3793-0.1373-0.05580.2815-0.1213-0.2289-0.3422-0.48880.05260.3662-0.2121-0.0667-0.0825-0.14490.0799-0.288161.874950.021314.2486
732.4544-21.931-15.19517.806310.043613.1578-0.0087-0.85570.614-0.15250.1939-0.2981-0.49760.3611-0.1851-0.26-0.0771-0.0706-0.2516-0.0112-0.395350.059456.80247.6395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 733 - 73
2X-RAY DIFFRACTION2AA74 - 11674 - 116
3X-RAY DIFFRACTION3AA117 - 138117 - 138
4X-RAY DIFFRACTION4BB3 - 133 - 13
5X-RAY DIFFRACTION5BB20 - 7320 - 73
6X-RAY DIFFRACTION6BB74 - 11674 - 116
7X-RAY DIFFRACTION7BB117 - 138117 - 138

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