[English] 日本語
Yorodumi
- PDB-3uxu: The structure of the catalytic domain of the Sulfolobus Spindle-s... -

+
Open data


ID or keywords:

Loading...

-
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 / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. ...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 / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / 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
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more