[English] 日本語
Yorodumi
- PDB-1a5t: CRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF THE CLAMP-LOADER ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a5t
TitleCRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF THE CLAMP-LOADER COMPLEX OF ESCHERICHIA COLI DNA POLYMERASE III
ComponentsDELTA PRIME
KeywordsZINC FINGER / DNA REPLICATION
Function / homology
Function and homology information


DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA replication / DNA-directed DNA polymerase activity / DNA clamp loader activity / DNA binding
Similarity search - Function
DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA polymerase III, delta subunit / : / Ubiquitin-associated (UBA) domain ...DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA polymerase III, delta subunit / : / Ubiquitin-associated (UBA) domain / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase III subunit delta'
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsGuenther, B. / Onrust, R. / Sali, A. / O'Donnell, M. / Kuriyan, J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III.
Authors: Guenther, B. / Onrust, R. / Sali, A. / O'Donnell, M. / Kuriyan, J.
#1: Journal: Thesis, The Rockefeller University / Year: 1996
Title: Structural Studies on the DNA Replication Apparatus: X-Ray Crystal Structure of the Delta-Prime Subunit of Escherichia Coli DNA Polymerase III
Authors: Guenther, B.D.
History
DepositionFeb 18, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DELTA PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0462
Polymers36,9801
Non-polymers651
Water3,639202
1
A: DELTA PRIME
hetero molecules

A: DELTA PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0924
Polymers73,9612
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)98.900, 104.000, 75.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein DELTA PRIME / HOLB


Mass: 36980.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Cellular location: CYTOPLASM / Gene: HOLB / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / pH: 6.8
Details: THE PROTEIN WAS CRYSTALLIZED FROM 20-27% PEG 400, 100 MM HEPES, PH6.8, 100 MM MGCL2, 1-3% GLYCEROL, 10MM MGSO4, AT 4C, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220-27 %PEG4001reservoir
3100 mMHEPES1reservoir
4100 mM1reservoirMgCl2
51-3 %glycerol1reservoir
610 mM1reservoirMgSO4

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 19389 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.074 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5 % / Mean I/σ(I) obs: 6 / Rsym value: 0.353 / % possible all: 93
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.353

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: INFORMATION FOR THE ZINC AND ZN-S INTERACTIONS WERE INCORPORATED INTO THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.265 -10 %RANDOM
Rwork0.205 ---
obs0.205 17778 88 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 1 202 2715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.15
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
Rfactor% reflection
Rfree0.285 6.8 %
Rwork0.233 -
obs-74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 18759 / Rfactor all: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.233

+
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