[English] 日本語
Yorodumi
- PDB-4im9: Cystal structure of DnaG primase C-terminal domain from Vibrio ch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4im9
TitleCystal structure of DnaG primase C-terminal domain from Vibrio cholerae
ComponentsDNA primase
KeywordsTRANSFERASE / helicase-primase complex / DNA replication / Hair pin helix / helicase binding
Function / homologyDNAb Helicase; Chain A / DNAb Helicase; Chain A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsAbdul Rehman, S.A. / Tarique, K.F. / Gourinath, S.
CitationJournal: To be Published
Title: Cystal structure of DnaG primase C-terminal domain from Vibrio cholerae
Authors: Abdul Rehman, S.A. / Tarique, K.F. / Gourinath, S.
History
DepositionJan 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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_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
A: DNA primase
B: DNA primase
C: DNA primase


Theoretical massNumber of molelcules
Total (without water)53,1213
Polymers53,1213
Non-polymers00
Water77543
1
A: DNA primase


Theoretical massNumber of molelcules
Total (without water)17,7071
Polymers17,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA primase


Theoretical massNumber of molelcules
Total (without water)17,7071
Polymers17,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA primase


Theoretical massNumber of molelcules
Total (without water)17,7071
Polymers17,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.412, 73.779, 132.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA primase


Mass: 17706.951 Da / Num. of mol.: 3 / Fragment: Primase C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: C-terminal domain, dnaG, Primase, VC395_0535 / Plasmid: pET28(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C3LX44, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium cacodylate trihydrate (pH 6.5), 0.2 M MgCl2, 30% W/v PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97872 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2012 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→66.326 Å / Num. all: 25083 / Num. obs: 25046 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1189 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.46→66.326 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.048 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26369 1280 5.1 %RANDOM
Rwork0.22692 ---
obs0.22885 23822 99.8 %-
all-25083 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2---1.59 Å20 Å2
3---0.91 Å2
Refine analyzeLuzzati coordinate error obs: 0.3683 Å
Refinement stepCycle: LAST / Resolution: 2.46→66.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 0 43 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193293
X-RAY DIFFRACTIONr_angle_refined_deg1.5522.0014455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8325.29155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88215627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5461522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212410
LS refinement shellResolution: 2.457→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 84 -
Rwork0.298 1546 -
obs--97.49 %

+
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