[English] 日本語
Yorodumi
- PDB-6t66: Crystal structure of the Vibrio cholerae replicative helicase (Dn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t66
TitleCrystal structure of the Vibrio cholerae replicative helicase (DnaB) with GDP-AlF4
ComponentsReplicative DNA helicase
KeywordsREPLICATION / Helicase
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Replicative DNA helicase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsLegrand, P. / Quevillon-Cheruel, S. / Li de la Sierra-Gallay, I. / Walbott, H.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase.
Authors: Marsin, S. / Adam, Y. / Cargemel, C. / Andreani, J. / Baconnais, S. / Legrand, P. / Li de la Sierra-Gallay, I. / Humbert, A. / Aumont-Nicaise, M. / Velours, C. / Ochsenbein, F. / Durand, D. ...Authors: Marsin, S. / Adam, Y. / Cargemel, C. / Andreani, J. / Baconnais, S. / Legrand, P. / Li de la Sierra-Gallay, I. / Humbert, A. / Aumont-Nicaise, M. / Velours, C. / Ochsenbein, F. / Durand, D. / Le Cam, E. / Walbott, H. / Possoz, C. / Quevillon-Cheruel, S. / Ferat, J.L.
History
DepositionOct 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase
E: Replicative DNA helicase
F: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,04924
Polymers317,6266
Non-polymers3,42318
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41100 Å2
ΔGint-273 kcal/mol
Surface area106340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.978, 123.292, 263.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Replicative DNA helicase


Mass: 52937.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: dnaB, BC353_11625, C9J66_17780, ERS013165_03687, ERS013200_03939, ERS013206_03692, F0315_03560, FLM02_14585, HPY05_12185
Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A085R2T8, DNA helicase
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10% (v/v) MPD 0.1 M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2019 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.9→49.63 Å / Num. obs: 38678 / % possible obs: 99.8 % / Redundancy: 18.3 % / Biso Wilson estimate: 147.24 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.055 / Rrim(I) all: 0.293 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
3.9-4.0715.53.8624940.3141.00997.7
17.65-49.6215.70.084400.9970.02294.90.083

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSMar 15, 2019data reduction
XDSMar 15, 2019data scaling
MOLREPVers 11.7.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QEL

6qel


Resolution: 3.9→49.63 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.01 / Details: Dataset anisotropically truncated by STARANISO
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1373 5.07 %RANDOM
Rwork0.255 ---
obs0.256 27099 75.2 %-
Displacement parametersBiso max: 299.97 Å2 / Biso mean: 199.03 Å2 / Biso min: 34.77 Å2
Baniso -1Baniso -2Baniso -3
1-6.1779 Å20 Å20 Å2
2---5.2436 Å20 Å2
3----0.9344 Å2
Refine analyzeLuzzati coordinate error obs: 0.79 Å
Refinement stepCycle: final / Resolution: 3.9→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20618 0 204 0 20822
Biso mean--182.34 --
Num. residues----2644
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7692SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3724HARMONIC5
X-RAY DIFFRACTIONt_it21116HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2816SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23798SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d21116HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg28592HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion1.53
X-RAY DIFFRACTIONt_other_torsion21.71
LS refinement shellResolution: 3.9→4.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2575 26 4.8 %
Rwork0.2325 516 -
all0.2336 542 -
obs--13.07 %
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)
11.67732.5572-2.91041.4322-1.59493.36180.00280.01510.0002-0.15010.0429-0.1087-0.06160.0643-0.0457-0.0651-0.07380.1511-0.09450.09250.0027-5.5492-24.586426.057
23.14040.5547-2.91042.03971.353.7282-0.01760.0613-0.07630.03360.00580.1050.0223-0.02580.0118-0.0618-0.06090.152-0.03750.138-0.1028-40.8807-33.174952.1707
32.21732.6180.63855.73230.86481.0336-0.0079-0.0460.0149-0.02130.05970.005-0.0125-0.1519-0.05180.2480.0831-0.1199-0.0210.01590.0444-30.90191.080664.51
47.28070.4773-2.88227.315-0.6233.6160.0114-0.02650.2110.03870.019-0.1422-0.18630.0507-0.03040.3024-0.0358-0.05470.1779-0.1520.2686-5.015236.559772.5815
54.7789-0.7799-1.82496.71562.91044.435-0.023-0.03380.13570.10570.0148-0.0012-0.17190.01020.00820.12530.0428-0.08560.0206-0.14760.219314.031621.596743.44
67.2341.30861.24927.44452.73693.8637-0.00760.1181-0.0347-0.08130.0335-0.12850.11970.0189-0.02590.1171-0.07860.056-0.0464-0.1340.168227.664-10.666915.4597
74.3482-0.3516-2.91043.01920.33383.1287-0.00120.006-0.1955-0.2159-0.12040.13140.0184-0.00310.1217-0.0786-0.05-0.0615-0.3036-0.0032-0.3009-41.7968-7.681715.7151
82.97680.7791-1.36783.51680.6172.9609-0.03590.1014-0.0298-0.2316-0.01150.21570.053-0.15720.0474-0.3040.00490.0865-0.3039-0.152-0.304-51.455112.700634.8306
94.72260.91-2.60545.61371.91854.5735-0.0540.01980.21050.03250.04630.1804-0.1905-0.02230.0076-0.304-0.0603-0.152-0.304-0.1455-0.304-36.815837.352840.6023
106.5862.479-2.77662.716-1.20682.5002-0.01110.21940.2324-0.28170.0715-0.2179-0.2550.1434-0.0603-0.304-0.0374-0.0751-0.1426-0.05210.0157-13.452245.624524.3117
111.6498-1.4523-2.6211.24692.91045.46420.0049-0.11840.15280.207-0.13950.0304-0.0442-0.04830.13470.304-0.1520.1520.2084-0.03090.3040.244422.74375.1927
122.52342.91040.68888.31552.59891.77050.01940.11390.16160.1028-0.03530.3502-0.2174-0.26430.01590.2247-0.00740.152-0.11110.06520.2872-17.67270.4447-2.489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|22 - A|171 }A22 - 171
2X-RAY DIFFRACTION2{ B|22 - B|171 }B22 - 171
3X-RAY DIFFRACTION3{ C|22 - C|171 }C22 - 171
4X-RAY DIFFRACTION4{ D|22 - D|171 }D22 - 171
5X-RAY DIFFRACTION5{ E|22 - E|171 }E22 - 171
6X-RAY DIFFRACTION6{ F|21 - F|171 }F21 - 171
7X-RAY DIFFRACTION7{ A|199 - A|461 F|172 - F|198 }A199 - 461
8X-RAY DIFFRACTION7{ A|199 - A|461 F|172 - F|198 }F172 - 198
9X-RAY DIFFRACTION8{ B|199 - B|462 A|172 - A|198 }B199 - 462
10X-RAY DIFFRACTION8{ B|199 - B|462 A|172 - A|198 }A172 - 198
11X-RAY DIFFRACTION9{ C|199 - C|461 B|172 - B|198 }C199 - 461
12X-RAY DIFFRACTION9{ C|199 - C|461 B|172 - B|198 }B172 - 198
13X-RAY DIFFRACTION10{ D|199 - D|462 C|172 - C|198 }D199 - 462
14X-RAY DIFFRACTION10{ D|199 - D|462 C|172 - C|198 }C172 - 198
15X-RAY DIFFRACTION11{ E|199 - E|461 D|172 - D|198 }E199 - 461
16X-RAY DIFFRACTION11{ E|199 - E|461 D|172 - D|198 }D172 - 198
17X-RAY DIFFRACTION12{ F|199 - F|462 E|172 - E|198 }F199 - 462
18X-RAY DIFFRACTION12{ F|199 - F|462 E|172 - E|198 }E172 - 198

+
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://pdbjlvh1.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