[English] 日本語
Yorodumi
- PDB-8czq: The crystal structure of MtbTOP1 in complex with both G- and T-se... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8czq
TitleThe crystal structure of MtbTOP1 in complex with both G- and T-segments
Components
  • DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')
  • DNA topoisomerase 1
KeywordsISOMERASE/DNA / topoisomerase 1 / MYCOBACTERIUM TUBERCULOSIS / G-segment / T-segment / 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 / DNA binding / metal ion binding
Similarity search - Function
Topoisomerase C-terminal repeat / Topoisomerase C-terminal repeat / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. ...Topoisomerase C-terminal repeat / Topoisomerase C-terminal repeat / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsTan, K. / Tse-Dinh, Y.-C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01GM054226 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM139817 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: The interaction between transport-segment DNA and topoisomerase IA-crystal structure of MtbTOP1 in complex with both G- and T-segments.
Authors: Ferdous, S. / Dasgupta, T. / Annamalai, T. / Tan, K. / Tse-Dinh, Y.C.
History
DepositionMay 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 1
B: DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')
C: DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')
D: DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,70017
Polymers88,6124
Non-polymers1,08813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-54 kcal/mol
Surface area37750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.501, 98.632, 104.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein DNA topoisomerase 1 / DNA topoisomerase I


Mass: 77843.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: topA_1, topA, BN1213_00605, BN1303_02614, ERS013471_01645, ERS027644_01463, ERS124361_02532, RN05_3882
Plasmid: ET-HIS6-MOCR TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): T7 EXPRESS CRYSTAL / References: UniProt: A0A0E8VY41, EC: 5.99.1.2
#2: DNA chain DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')


Mass: 3589.341 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M sodium acetate, trihydrate, 12% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 5, 2017 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.78→46.5 Å / Num. obs: 24480 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 82.81 Å2 / CC1/2: 0.982 / CC star: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Net I/av σ(I): 1.138 / Net I/σ(I): 23.5
Reflection shellResolution: 2.78→2.83 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.372 / Num. unique obs: 1195 / CC1/2: 0.49 / CC star: 0.811 / R split: 1.15 / Rpim(I) all: 0.614 / Χ2: 0.642 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CQI

6cqi


Resolution: 2.78→46.25 Å / SU ML: 0.4265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2685 1198 4.91 %
Rwork0.2476 23197 -
obs0.2486 24395 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.97 Å2
Refinement stepCycle: LAST / Resolution: 2.78→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 698 62 0 5690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035848
X-RAY DIFFRACTIONf_angle_d0.55758082
X-RAY DIFFRACTIONf_chiral_restr0.0383913
X-RAY DIFFRACTIONf_plane_restr0.0058940
X-RAY DIFFRACTIONf_dihedral_angle_d18.41281068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.890.40691170.38892469X-RAY DIFFRACTION95.28
2.89-3.020.35381250.3332509X-RAY DIFFRACTION99.36
3.02-3.180.33381490.28812549X-RAY DIFFRACTION99.45
3.18-3.380.29751560.29212524X-RAY DIFFRACTION99.7
3.38-3.640.33171450.27842556X-RAY DIFFRACTION99.82
3.64-4.010.26691580.23582557X-RAY DIFFRACTION99.89
4.01-4.590.2255940.21612631X-RAY DIFFRACTION99.89
4.59-5.780.21921400.23042643X-RAY DIFFRACTION99.96
5.78-46.250.25751140.23242759X-RAY DIFFRACTION99.17
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)
11.659359674020.9275340635110.4113946899313.278580082250.8899977378861.32372102687-0.08092266021410.1586608082970.119521887393-0.258627601110.0446854675728-0.0599775322078-0.1074043807510.2239426696590.04476318713920.3249268912760.06479326245160.03555207807480.3660936654080.08578771516940.50185475163833.430340821713.336755007549.0038134665
23.571117918821.522868365863.116226305823.097539241070.9578792300266.00729558466-0.4195533900991.074402973170.302086878643-0.796070391650.4428095644390.108423854123-0.7576714741370.7846839321280.03946517302640.894978032966-0.200527398857-0.06150653539380.8202099633910.08481563217340.79575636927436.400644928129.377610993524.4688997483
31.614938515310.0167004284921-1.212993899192.534708726750.4765457825324.46363894436-0.1981490879580.2977058935610.0735416884898-0.3487974529380.09626041054870.4605130470430.145736514936-0.3006479593980.08450982422180.3754928231650.0141203541813-0.1528670359750.4661622753490.07496205523270.51902843694122.1910913077-1.2331910480737.2460087238
46.553254369182.75947037680.5336365174168.68384569659-0.1253286948165.815984010520.105740792769-0.150453892034-0.726189113805-0.1104297379310.0369758859946-1.56197287686-0.1996551694441.55397782021-0.2397170793460.512379989651-0.01916089882040.1443440905730.759783944875-0.06327224334430.73487072606941.92163413848.7457025620652.0727154508
53.62512458675-3.952767511381.91237433687.504912182520.241987148936.66554637903-0.01230026536851.630323944940.705105755411-0.175367921657-0.178507106468-0.318765291849-0.0238487777697-0.05333149392220.2183723628910.517799096556-0.135186725367-0.1343504420721.042950148860.01588883145710.98338994104138.77417900196.2524039523316.0297306211
67.29387654169-6.355580043323.435933146988.73885762844-0.5997884996273.355561749320.163869931732-0.932892588189-0.590978818546-0.2593001864710.1735359205361.32130159750.255353420877-1.1315329448-0.4165617550780.835545703721-0.293786706803-0.09766128438091.485402285090.4812772671740.98968177652937.583339223910.408856834916.9777527207
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 16 through 273 )AA16 - 2731 - 244
22chain 'A' and (resid 274 through 494 )AA274 - 494245 - 445
33chain 'A' and (resid 495 through 704 )AA495 - 704446 - 655
44chain 'B' and (resid 1 through 12 )BB1 - 12
55chain 'C' and (resid 1 through 12 )CC1 - 12
66chain 'D' and (resid 2 through 12 )DD2 - 12

+
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