[English] 日本語
Yorodumi
- PDB-2h7f: Structure of variola topoisomerase covalently bound to DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h7f
TitleStructure of variola topoisomerase covalently bound to DNA
Components
  • 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'
  • 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'
  • DNA topoisomerase 1Topoisomerase
KeywordsISOMERASE/DNA / type IB topoisomerase / dna binding / protein-dna complex / isomerase / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / virion component / DNA binding
Similarity search - Function
DNA topoisomerase I, N-terminal, viral / Viral DNA topoisomerase I, N-terminal / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / Topoisomerase (Topo) IB-type catalytic domain profile. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. ...DNA topoisomerase I, N-terminal, viral / Viral DNA topoisomerase I, N-terminal / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / Topoisomerase (Topo) IB-type catalytic domain profile. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type / Eukaryotic DNA topoisomerase I, catalytic core / DNA breaking-rejoining enzyme, catalytic core / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesVariola virus (smallpox virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsPerry, K. / Hwang, Y. / Bushman, F.D. / Van Duyne, G.D.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural basis for specificity in the poxvirus topoisomerase.
Authors: Perry, K. / Hwang, Y. / Bushman, F.D. / Van Duyne, G.D.
History
DepositionJun 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Y: 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'
Z: 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'
X: DNA topoisomerase 1


Theoretical massNumber of molelcules
Total (without water)44,3263
Polymers44,3263
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.523, 138.232, 113.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11X-327-

HOH

-
Components

#1: DNA chain 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'


Mass: 3291.145 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'


Mass: 4337.855 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA topoisomerase 1 / Topoisomerase / E.C.5.99.1.2 / DNA topoisomerase I


Mass: 36697.430 Da / Num. of mol.: 1 / Mutation: C100S, C211S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variola virus (smallpox virus) / Genus: Orthopoxvirus / Gene: TOP1 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32989, DNA topoisomerase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% PEG 8000, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Tris-HClTris11
3H2O11
4PEG 800012
5Tris-HClTris12
6H2O12

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.97917
SYNCHROTRONALS 8.2.120.97952, 0.97935, 0.96394
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 12, 2005
ADSC QUANTUM 42CCDApr 12, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.979521
30.979351
40.963941
Reflection

D res high: 2.9 Å / D res low: 50 Å / Redundancy: 4.3 %

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
115.7721210.0691.531174797.5
215.7745360.0711.531177397.7
315.3743200.0681.411176897.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.635090.910.0512.1444.1
5.276.639610.0682.3824.3
4.65.2797.110.0612.054.3
4.184.697.510.0611.7964.3
3.884.1898.110.0711.7964.2
3.653.8898.610.0821.5914.3
3.473.6598.810.0941.4664.3
3.323.4798.610.1151.2564.3
3.193.3298.910.1461.1114.3
3.083.1998.510.2171.0014.4
2.993.0899.210.2940.9224.3
2.92.9998.710.3350.8734.3
6.635091.520.0522.1064.1
5.276.6396.120.0672.2794.3
4.65.2797.120.0612.014.3
4.184.697.720.0621.7924.3
3.884.1898.220.0721.8114.2
3.653.8898.920.0841.5974.3
3.473.6598.820.0981.5314.3
3.323.4798.820.1181.2844.3
3.193.3299.120.1521.1474.3
3.083.1998.820.2160.9984.4
2.993.0899.420.2980.9234.3
2.92.999920.3470.914.3
6.635091.630.0461.84.1
5.276.639630.0631.9454.3
4.65.279730.0581.7754.3
4.184.697.430.0591.6454.3
3.884.1898.230.071.6924.2
3.653.8898.830.0831.5234.3
3.473.6598.830.0961.4194.3
3.323.4798.930.1181.2584.3
3.193.3299.130.1531.1174.3
3.083.1998.830.2250.9944.4
2.993.0899.330.3070.9144.3
2.92.999930.3570.8874.3
ReflectionResolution: 2.7→50 Å / Num. obs: 14945 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.038 / Χ2: 1.212 / Net I/σ(I): 29.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.784.30.19912141.2661,299.8
2.78-2.874.30.15212311.4431,299.8
2.87-2.974.40.11712381.21,299.8
2.97-3.094.30.09512241.2771,299.7
3.09-3.234.30.0712391.1391,299.8
3.23-3.44.30.05412191.1591,299.8
3.4-3.614.30.04312481.2661,299.7
3.61-3.894.20.04312471.7391,299.9
3.89-4.294.30.03112461.0341,299.7
4.29-4.94.30.03212521.1481,299.5
4.9-6.184.30.02912741.0051,299.5
6.18-504.10.03413130.8841,297.7

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.98 Å / D res low: 20 Å / FOM : 0.42 / Reflection: 10709
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97934.51-8.35
13 wavelength20.97954.36-10.18
13 wavelength30.96393.21-5.26
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.1910.2210.0430.556
2Se600.030.2780.0980.621
3Se600.1450.2820.1010.699
4Se600.2210.1480.1550.575
5Se600.8210.2260.0830.547
6Se600.3620.1230.1120.425
7Se600.0780.2340.0150.449
8Se600.1440.0090.0860.384
9Se600.4250.4870.0530.278
Phasing MAD shell
Resolution (Å)FOM Reflection
9.87-200.55571
6.53-9.870.62900
5.2-6.530.551129
4.44-5.20.471338
3.94-4.440.431496
3.58-3.940.41637
3.3-3.580.331762
3.08-3.30.251876

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 24.213 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.725 / ESU R Free: 0.307
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.237 770 5.1 %RANDOM
Rwork0.191 ---
all0.193 ---
obs0.193 15090 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.984 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2--4.04 Å20 Å2
3----2.74 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 505 0 54 3144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223231
X-RAY DIFFRACTIONr_angle_refined_deg1.532.1714469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7215313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07323.697119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16415505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.931515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022200
X-RAY DIFFRACTIONr_nbd_refined0.2250.21323
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22174
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.26
X-RAY DIFFRACTIONr_mcbond_it0.521.51610
X-RAY DIFFRACTIONr_mcangle_it0.91522566
X-RAY DIFFRACTIONr_scbond_it1.22931989
X-RAY DIFFRACTIONr_scangle_it1.9824.51903
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 56 -
Rwork0.315 1047 -
obs-1103 99.91 %
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)
18.00032.6217-2.173510.49242.34766.5469-0.20870.0486-1.13350.0759-0.18240.41881.7735-0.44140.39110.4163-0.30410.1107-0.1459-0.13910.1603-9.5229-2.620414.7187
25.8249-0.3012-0.77783.7414-0.23774.7873-0.02490.17650.2524-0.0167-0.2104-0.1546-0.27730.3780.2353-0.2903-0.0979-0.0619-0.2080.0228-0.36519.189529.034412.2459
33.6644-0.51930.79153.747-0.39296.47530.0550.2887-0.2132-0.38670.19760.88720.2026-0.6769-0.2526-0.1359-0.14690.0225-0.1391-0.102-0.0926-8.932717.48619.3722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 74
2X-RAY DIFFRACTION2X75 - 314
3X-RAY DIFFRACTION3Y501 - 511

+
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