[English] 日本語
Yorodumi
- PDB-6jir: Crystal structure of C. crescentus beta sliding clamp with PEG bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jir
TitleCrystal structure of C. crescentus beta sliding clamp with PEG bound to putative beta-motif tethering region
ComponentsBeta sliding clamp
KeywordsTRANSFERASE / Caulobacter crescentus / peptide bound / homodimer
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / :
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Beta sliding clamp
Similarity search - Component
Biological speciesCaulobacter vibrioides CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJiang, X. / Teng, M. / Li, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31130018 China
Ministry of Science and Technology (China)2012CB917200 China
National Natural Science Foundation of China31370732, 31270014 and U1432107 China
CitationJournal: Febs J. / Year: 2020
Title: Caulobacter crescentus beta sliding clamp employs a noncanonical regulatory model of DNA replication.
Authors: Jiang, X. / Zhang, L. / An, J. / Wang, M. / Teng, M. / Guo, Q. / Li, X.
History
DepositionFeb 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: 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 1.2Nov 22, 2023Group: 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: Beta sliding clamp
B: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,06011
Polymers85,1192
Non-polymers9419
Water6,557364
1
A: Beta sliding clamp
hetero molecules

A: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,36414
Polymers85,1192
Non-polymers1,24512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2450 Å2
ΔGint-3 kcal/mol
Surface area33800 Å2
MethodPISA
2
B: Beta sliding clamp
hetero molecules

B: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7558
Polymers85,1192
Non-polymers6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2510 Å2
ΔGint0 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.724, 123.527, 85.975
Angle α, β, γ (deg.)90.00, 120.01, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Beta sliding clamp / Sliding clamp


Mass: 42559.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides CB15 (bacteria) / Gene: dnaN / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0CAU5

-
Non-polymers , 6 types, 373 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25 % PEG1000, 0.2 M NaCl and 0.1 M Na/K phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 74116 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Net I/σ(I): 27.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4 / Num. unique obs: 3421 / Rsym value: 0.194 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TR8

4tr8


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.764 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3737 5.04 %RANDOM
Rwork0.171 ---
obs-74116 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å2-0.35 Å2
2---1.59 Å20 Å2
3---0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5660 0 62 364 6086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195824
X-RAY DIFFRACTIONr_bond_other_d0.0060.025703
X-RAY DIFFRACTIONr_angle_refined_deg1.51.997896
X-RAY DIFFRACTIONr_angle_other_deg0.94313101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62423.648244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99515958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6281551
X-RAY DIFFRACTIONr_chiral_restr0.0920.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4933.1363012
X-RAY DIFFRACTIONr_mcbond_other2.4913.1363011
X-RAY DIFFRACTIONr_mcangle_it2.5984.6923758
X-RAY DIFFRACTIONr_mcangle_other2.5994.6933759
X-RAY DIFFRACTIONr_scbond_it2.6033.4662812
X-RAY DIFFRACTIONr_scbond_other2.6043.4672813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5225.054139
X-RAY DIFFRACTIONr_long_range_B_refined2.71924.926254
X-RAY DIFFRACTIONr_long_range_B_other2.69524.7676137
X-RAY DIFFRACTIONr_rigid_bond_restr4.611311527
X-RAY DIFFRACTIONr_sphericity_free11.8035118
X-RAY DIFFRACTIONr_sphericity_bonded4.519511687
LS refinement shellResolution: 1.948→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 267 -
Rwork0.207 5119 -
obs--98.23 %

+
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