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- PDB-5dor: P2 Integrase catalytic domain in space group P21 -

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Basic information

Entry
Database: PDB / ID: 5dor
TitleP2 Integrase catalytic domain in space group P21
ComponentsIntegrase
KeywordsHYDROLASE / tyrosine recombinase / integrase
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
Intergrase catalytic core / hpI Integrase; Chain A / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / 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 speciesEnterobacteria phage P2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSkaar, K. / Claesson, M. / Odegrip, R. / Haggard-Ljungquist, E. / Hogbom, M.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2010-5200, 2014-5667 Sweden
Wenner-Gren Foundation Sweden
Carl Tryggers Foundation Sweden
CitationJournal: Febs Lett. / Year: 2015
Title: Crystal structure of the bacteriophage P2 integrase catalytic domain.
Authors: Skaar, K. / Claesson, M. / Odegrip, R. / Hogbom, M. / Haggard-Ljungquist, E. / Stenmark, P.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4356
Polymers78,2744
Non-polymers1602
Water1,33374
1
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2984
Polymers39,1372
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-78 kcal/mol
Surface area15830 Å2
MethodPISA
2
C: Integrase
D: Integrase


Theoretical massNumber of molelcules
Total (without water)39,1372
Polymers39,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-31 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.110, 92.225, 64.937
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLUGLUAA162 - 3281 - 167
21THRTHRGLUGLUBB162 - 3281 - 167
12GLYGLYTHRTHRAA163 - 3252 - 164
22GLYGLYTHRTHRCC163 - 3252 - 164
13GLYGLYGLUGLUAA163 - 3282 - 167
23GLYGLYGLUGLUDD163 - 3282 - 167
14GLYGLYTHRTHRBB163 - 3252 - 164
24GLYGLYTHRTHRCC163 - 3252 - 164
15GLYGLYGLUGLUBB163 - 3282 - 167
25GLYGLYGLUGLUDD163 - 3282 - 167
16GLYGLYGLUGLUCC163 - 3262 - 165
26GLYGLYGLUGLUDD163 - 3262 - 165

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Integrase /


Mass: 19568.572 Da / Num. of mol.: 4 / Fragment: Catalytic domain, UNP residues 162-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P2 (virus) / Gene: int / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36932
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Zinc Chloride, Tris, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.2782 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 2.5→64.54 Å / Num. obs: 26038 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.759 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C6K
Resolution: 2.5→64.54 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 30.84 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 0.626 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 1328 5.1 %RANDOM
Rwork0.22954 ---
obs0.2318 24692 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.041 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å22.45 Å2
2--1.99 Å20 Å2
3----6.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 6 74 5058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195090
X-RAY DIFFRACTIONr_bond_other_d0.0060.025024
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9616876
X-RAY DIFFRACTIONr_angle_other_deg1.298311504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4545628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13622.67221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.20215879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6611545
X-RAY DIFFRACTIONr_chiral_restr0.0760.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215660
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021185
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_it1.411.6732545
X-RAY DIFFRACTIONr_mcbond_other1.4021.6712544
X-RAY DIFFRACTIONr_mcangle_it2.4032.4933162
X-RAY DIFFRACTIONr_mcangle_other2.4032.4973163
X-RAY DIFFRACTIONr_scbond_it1.2761.7822545
X-RAY DIFFRACTIONr_scbond_other1.161.7642539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.922.6133708
X-RAY DIFFRACTIONr_long_range_B_refined5.36213.2515873
X-RAY DIFFRACTIONr_long_range_B_other5.31313.2245866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A92310.1
12B92310.1
21A91660.09
22C91660.09
31A90460.1
32D90460.1
41B88930.12
42C88930.12
51B90750.09
52D90750.09
61C88070.11
62D88070.11
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 122 -
Rwork0.341 1772 -
obs--97.83 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
110.6993-4.0723-3.932810.2576-0.70749.6338-0.21920.2835-0.0433-0.1640.2064-0.2309-0.0606-0.32990.01280.09620.0756-0.15180.18290.00680.8876-51.739718.467543.0855
25.4468-2.03871.30044.5343-1.79077.1967-0.1982-0.7052-0.80.6660.42730.42040.6628-0.1295-0.22910.26610.1216-0.09430.27950.0420.9651-48.81313.30950.7488
36.5153-2.1364-0.77782.5482-1.6555.6205-0.3407-0.5406-0.58550.53570.25280.41070.6137-0.30070.08790.47790.0671-0.03570.40240.07541.011-47.77391.102251.8114
47.3635-2.9303-2.74042.38560.9872.0696-0.16740.4248-0.1344-0.04080.1420.45990.0206-0.44160.02540.06540.0378-0.20630.2988-0.03270.8957-52.05811.091638.9753
52.253-2.2278-6.880613.64555.932521.2677-0.4330.0386-0.12680.16120.4651-0.01881.4562-0.0154-0.03220.16420.0173-0.25570.3001-0.1871.1166-42.5721-2.076934.1771
610.0157-0.7646-3.47611.3190.4372.8240.09940.40560.2592-0.18130.10110.0222-0.3127-0.1661-0.20050.14620.0072-0.22730.168-0.09370.7806-29.01948.06627.0181
726.27098.6564-6.552919.09121.34893.1368-0.1268-0.8537-0.92020.73970.4557-0.14770.42460.3948-0.32890.14820.0978-0.17640.13270.00270.5073-15.9848-7.613228.4018
80.74320.4154-0.79215.682-0.23624.7725-0.0473-0.09720.4527-0.27850.2103-0.3479-0.22030.3501-0.16290.1306-0.0222-0.18390.0751-0.02150.6892-11.8025-1.317216.9267
96.5673-0.2269-0.17146.4353-1.27285.25090.37170.4080.8779-0.9253-0.1710.151-0.7063-0.354-0.20060.36750.0969-0.14580.06060.10540.7335-19.51269.961511.3965
103.0895-0.4192-0.73436.67380.3772.4790.1267-0.09130.4911-0.29390.0721-0.0358-0.0040.4349-0.19870.076-0.0098-0.15250.07860.00080.574-9.9942-5.912613.3698
114.2227-2.3402-1.08313.6622.092.6734-0.0070.05110.0440.2005-0.02710.24670.5573-0.26370.03420.2177-0.0206-0.21180.135-0.03420.7189-24.0445-2.11423.0697
125.4251-1.2855-0.38133.859-3.4477.94340.02350.33160.2394-0.152-0.17190.56850.5706-0.31270.14830.1565-0.0064-0.1720.1693-0.09210.729-32.0018-1.810423.9017
134.4969-0.90851.251326.92342.511914.45090.1259-0.32110.1306-0.332-0.1453-0.3940.26540.85880.01930.05950.0629-0.16340.2919-0.12330.6603-34.89167.23643.6648
1420.55577.830313.346623.1687-6.988415.8870.31961.0046-0.97510.63630.0785-0.8053-0.09680.8293-0.39810.05460.0666-0.20820.3177-0.2041.0614-41.626915.819548.0524
1522.35732.46549.6196.02694.36066.242-0.2923-0.49320.4386-0.2994-0.21930.213-0.4476-0.62020.51160.16380.2155-0.25920.6591-0.11840.56827.391843.586776.9803
165.7123-0.5984.16190.8719-0.44436.41680.4427-0.6939-0.47390.3706-0.1498-0.43250.6508-0.4198-0.29280.3014-0.1051-0.35380.34750.04130.673914.330928.79478.1288
1719.24433.0953-8.55939.0756-2.356616.3568-0.37570.9337-1.46460.35790.5541-0.16431.5355-1.1835-0.17850.36-0.0669-0.39330.3256-0.07210.813313.075319.641371.5535
183.6842-0.2433.70716.6212-0.680910.33230.0733-0.0625-0.34480.10570.1038-0.1610.53790.3375-0.17710.1269-0.0029-0.21960.3077-0.09740.720315.692626.692669.6843
1912.975-10.0535-1.915217.37149.98949.56220.0838-0.94580.04080.7222-0.0217-0.2250.5655-0.9432-0.06210.2317-0.1226-0.3020.50780.07870.513614.387533.178886.6623
204.4546-2.62431.16541.94160.0631.7437-0.5333-1.1183-0.47770.80320.17050.52050.7382-1.31620.36280.8525-0.26710.07741.4525-0.18370.85721.377238.647485.2036
216.7651-0.86642.08410.1172-0.23987.8720.1312-0.9157-0.33700.0630.03330.1998-0.8488-0.19420.1399-0.1125-0.22770.6020.040.59460.246629.163168.6241
224.5737-3.00843.876410.4623-10.273417.24090.0349-1.2029-0.3598-0.14250.37130.46670.0915-1.7871-0.40620.0579-0.0816-0.10780.7937-0.00710.615-7.572930.943868.1648
235.61452.35924.83142.8116-0.03648.5637-0.5918-0.022-0.0851-0.65020.25810.2713-0.80910.20130.33370.4675-0.1883-0.29340.34060.03840.6598-11.30831.4945.4314
2410.1478-2.27313.251410.69270.30319.296-0.1020.8907-0.6706-0.42910.5096-0.3603-0.11580.7831-0.40760.0611-0.0588-0.09730.1957-0.16280.8097-13.227817.723936.9021
259.95572.83486.50176.67192.3948.7938-0.5586-1.06990.2294-0.3676-0.18770.8215-0.3677-0.93390.74640.08920.0711-0.19680.2179-0.12350.6804-25.509524.744242.959
268.17115.21062.77437.13193.085212.1388-0.5715-1.0361.2817-0.403-0.18741.2874-1.3922-1.20050.75890.240.2092-0.32960.2984-0.21330.9471-23.792734.165246.0951
2710.1703-2.33723.6988.77462.28723.7238-0.2234-0.3004-0.318-0.07820.1769-0.0294-0.0869-0.02770.04650.0682-0.0396-0.15560.2663-0.070.7537-24.931815.437637.5557
2832.5201-13.7514-1.030317.7915.894320.00060.7873-0.7673-2.34081.461-0.22450.53672.2862-0.5827-0.56290.5363-0.3254-0.4311.11980.18941.4762-20.07287.932945.183
297.17863.39634.73164.6813.06554.80110.313-0.757-0.49380.2723-0.2042-0.05840.2156-0.6373-0.10880.0518-0.0316-0.15260.24270.01090.6521-12.477322.771851.6049
305.7912-3.6907-5.26013.91592.862132.0314-0.3067-1.4737-0.13661.1687-0.24730.3205-0.7814-1.19480.5540.6986-0.6029-0.07221.5965-0.10730.846-17.702824.554460.6617
3114.74474.27926.17589.75373.59489.86470.5463-1.3695-0.6561.0114-0.32550.14740.7814-1.1694-0.22080.1703-0.1091-0.16420.32310.18980.7122-9.592218.487757.9875
329.07445.371810.41135.79489.698716.8308-0.114-0.063-0.1497-0.24140.2247-0.2373-0.42210.2836-0.11070.0472-0.0544-0.12420.3145-0.02940.66179.005733.028463.0435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A162 - 178
2X-RAY DIFFRACTION2A179 - 211
3X-RAY DIFFRACTION3A212 - 247
4X-RAY DIFFRACTION4A248 - 289
5X-RAY DIFFRACTION5A290 - 298
6X-RAY DIFFRACTION6A299 - 326
7X-RAY DIFFRACTION7B162 - 168
8X-RAY DIFFRACTION8B169 - 199
9X-RAY DIFFRACTION9B200 - 232
10X-RAY DIFFRACTION10B233 - 263
11X-RAY DIFFRACTION11B264 - 290
12X-RAY DIFFRACTION12B291 - 310
13X-RAY DIFFRACTION13B311 - 319
14X-RAY DIFFRACTION14B320 - 326
15X-RAY DIFFRACTION15C163 - 177
16X-RAY DIFFRACTION16C178 - 206
17X-RAY DIFFRACTION17C207 - 219
18X-RAY DIFFRACTION18C220 - 235
19X-RAY DIFFRACTION19C240 - 255
20X-RAY DIFFRACTION20C256 - 269
21X-RAY DIFFRACTION21C270 - 297
22X-RAY DIFFRACTION22C298 - 310
23X-RAY DIFFRACTION23C311 - 326
24X-RAY DIFFRACTION24D163 - 178
25X-RAY DIFFRACTION25D179 - 204
26X-RAY DIFFRACTION26D205 - 235
27X-RAY DIFFRACTION27D240 - 261
28X-RAY DIFFRACTION28D262 - 267
29X-RAY DIFFRACTION29D268 - 290
30X-RAY DIFFRACTION30D291 - 298
31X-RAY DIFFRACTION31D299 - 308
32X-RAY DIFFRACTION32D309 - 326

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