[English] 日本語
Yorodumi
- PDB-1v1q: Crystal structure of PriB- a primosomal DNA replication protein o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v1q
TitleCrystal structure of PriB- a primosomal DNA replication protein of Escherichia coli
ComponentsPRIMOSOMAL REPLICATION PROTEIN N
KeywordsDNA BINDING / PRIMOSOME / DNA REPLICATION
Function / homology
Function and homology information


pre-primosome complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / response to radiation / single-stranded DNA binding / identical protein binding
Similarity search - Function
Primosomal replication protein PriB / Another single-strand binding protein family / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CYSTEINE / Primosomal replication protein N
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLiu, J.-H. / Chang, T.-W. / Huang, C.-Y. / Chang, M.-C. / Chen, S.-U. / Wu, H.-N. / Hsiao, C.-D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Prib- a Primosomal DNA Replication Protein of Escherichia Coli
Authors: Liu, J.-H. / Chang, T.-W. / Huang, C.-Y. / Chen, S.-U. / Wu, H.-N. / Chang, M.-C. / Hsiao, C.-D.
History
DepositionApr 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PRIMOSOMAL REPLICATION PROTEIN N
B: PRIMOSOMAL REPLICATION PROTEIN N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9475
Polymers29,5842
Non-polymers3633
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.322, 57.358, 97.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PRIMOSOMAL REPLICATION PROTEIN N


Mass: 14791.990 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET21B-PRIB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07013
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION GLY 103 VAL
Sequence detailsRESIDUES PRECEDING POSITION 1 OF EACH MOLECULE ARE FROM T7-TAG, AND RESIDUES AFTER POSITION 104 OF ...RESIDUES PRECEDING POSITION 1 OF EACH MOLECULE ARE FROM T7-TAG, AND RESIDUES AFTER POSITION 104 OF CHAIN A ARE FROM HIS-TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 33.7 %
Crystal growpH: 5.7 / Details: pH 5.70

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.0083, 1.0093, 0.9921, 1.0249
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00831
21.00931
30.99211
41.02491
ReflectionResolution: 2.1→23.17 Å / Num. obs: 13751 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→23.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 284509.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1092 10.2 %RANDOM
Rwork0.206 ---
obs0.206 10679 79.9 %-
Solvent computationSolvent model: FLAT / Bsol: 40.8918 Å2 / ksol: 0.312944 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.86 Å20 Å20 Å2
2---6.54 Å20 Å2
3----2.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→23.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 21 134 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.931.5
X-RAY DIFFRACTIONc_mcangle_it3.432
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 122 9.6 %
Rwork0.228 1147 -
obs--58.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.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