[English] 日本語
Yorodumi
- PDB-2vye: Crystal Structure of the DnaC-ssDNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vye
TitleCrystal Structure of the DnaC-ssDNA complex
Components
  • 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'
  • REPLICATIVE DNA HELICASE
KeywordsHYDROLASE/DNA / HYDROLASE / DNA REPLICATION / NUCLEOTIDE-BINDING / DNAC / HELICASE / ATP-BINDING / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding
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. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / Replicative DNA helicase
Similarity search - Component
Biological speciesGEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsLo, Y.H. / Tsai, K.L. / Sun, Y.J. / Hsiao, C.D.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The Crystal Structure of a Replicative Hexameric Helicase Dnac and its Complex with Single-Stranded DNA.
Authors: Lo, Y.H. / Tsai, K.L. / Sun, Y.J. / Chen, W.T. / Huang, C.Y. / Hsiao, C.D.
History
DepositionJul 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
C: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)104,3563
Polymers104,3563
Non-polymers00
Water0
1
A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
C: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'

A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
C: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'

A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
C: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'


Theoretical massNumber of molelcules
Total (without water)313,0689
Polymers313,0689
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area35350 Å2
ΔGint-177.1 kcal/mol
Surface area155010 Å2
MethodPQS
Unit cell
Length a, b, c (Å)180.830, 180.830, 104.112
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein REPLICATIVE DNA HELICASE / DNAC


Mass: 50831.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
Production host: ESCHERICHIA COLI BL21 (bacteria)
References: UniProt: Q5KU75, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3' / SSDT15


Mass: 2692.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.45 Å3/Da / Density % sol: 77.26 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→30 Å / Num. obs: 14077 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.3
Reflection shellResolution: 4.1→4.25 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VYF

2vyf


Resolution: 4.1→29.94 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 157515.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.374 1213 10.3 %RANDOM
Rwork0.302 ---
obs0.302 11729 76.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 230.59 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 186.7 Å2
Baniso -1Baniso -2Baniso -3
1--42.1 Å260.23 Å20 Å2
2---42.1 Å20 Å2
3---84.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.75 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a1.33 Å1.01 Å
Refinement stepCycle: LAST / Resolution: 4.1→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 177 0 0 6439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4.1→4.36 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 126 9.5 %
Rwork0.306 1205 -
obs--52.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMION.TOP

+
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