[English] 日本語
Yorodumi
- PDB-8ac8: The nucleoprotein complex of Rep protein with DUE ssDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ac8
TitleThe nucleoprotein complex of Rep protein with DUE ssDNA
Components
  • DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')
  • Replication initiation protein
KeywordsDNA BINDING PROTEIN / Replication initiation protein Nucleoprotein complex Nucleic acid binding DNA binding
Function / homology
Function and homology information


plasmid maintenance / DNA replication initiation / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Initiator Rep protein, WH2 / Initiator Rep protein / Initiator Replication protein, WH1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / Replication initiation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNowacka, M. / Wegrzyn, K. / Oliwa, M. / Konieczny, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/D/NZ1/00239 Poland
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation.
Authors: Wegrzyn, K. / Oliwa, M. / Nowacka, M. / Zabrocka, E. / Bury, K. / Purzycki, P. / Czaplewska, P. / Pipka, J. / Giraldo, R. / Konieczny, I.
History
DepositionJul 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Replication initiation protein
A: Replication initiation protein
B: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')
D: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)64,1274
Polymers64,1274
Non-polymers00
Water5,891327
1
C: Replication initiation protein
D: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,0632
Polymers32,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area11360 Å2
2
A: Replication initiation protein
B: DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,0632
Polymers32,0632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-12 kcal/mol
Surface area11150 Å2
Unit cell
Length a, b, c (Å)47.400, 85.310, 146.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-372-

HOH

31A-416-

HOH

-
Components

#1: Protein Replication initiation protein / Protein E / Protein rep / Protein F4


Mass: 29343.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: repE, E, rep, ECOK12F045 / Production host: Escherichia coli (E. coli) / References: UniProt: P03856
#2: DNA chain DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*TP*A)-3')


Mass: 2719.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, ethylene glycol, HEPES, halogens

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.6→36.85 Å / Num. obs: 79263 / % possible obs: 99.6 % / Redundancy: 12.99 % / Biso Wilson estimate: 33.07 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.92
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 12422 / CC1/2: 0.431

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1REP

1rep


Resolution: 1.6→36.85 Å / SU ML: 0.2999 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.0221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 1988 2.53 %
Rwork0.2121 76610 -
obs0.2129 78598 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 334 0 327 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624124
X-RAY DIFFRACTIONf_angle_d0.82775673
X-RAY DIFFRACTIONf_chiral_restr0.0535614
X-RAY DIFFRACTIONf_plane_restr0.0056668
X-RAY DIFFRACTIONf_dihedral_angle_d28.5514701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.45461270.43024954X-RAY DIFFRACTION90.47
1.64-1.680.41321380.38975385X-RAY DIFFRACTION99.44
1.68-1.730.40841420.36385418X-RAY DIFFRACTION99.8
1.73-1.790.35081410.32645441X-RAY DIFFRACTION99.84
1.79-1.850.33231420.28565469X-RAY DIFFRACTION99.82
1.85-1.930.27641420.26165441X-RAY DIFFRACTION99.91
1.93-2.020.28491420.25415471X-RAY DIFFRACTION99.95
2.02-2.120.29761420.23255494X-RAY DIFFRACTION99.95
2.12-2.260.25821430.21565495X-RAY DIFFRACTION99.95
2.26-2.430.24941420.21745485X-RAY DIFFRACTION99.98
2.43-2.670.26641440.20965538X-RAY DIFFRACTION100
2.67-3.060.24951450.21025570X-RAY DIFFRACTION99.97
3.06-3.860.20361450.18975608X-RAY DIFFRACTION99.98
3.86-36.850.21561530.18665841X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: 0.205163594144 Å / Origin y: 20.4154722962 Å / Origin z: 0.528084942233 Å
111213212223313233
T0.201574691192 Å20.0308094389933 Å20.00220673330571 Å2-0.253834502072 Å20.0144120630881 Å2--0.280592038859 Å2
L0.0419424365568 °20.148673909001 °2-0.0171372250593 °2-0.861282933284 °20.456651789469 °2--0.848853726453 °2
S-0.0219043013923 Å °-0.00522704928218 Å °-0.0355938720481 Å °0.00101681858836 Å °0.00928853962632 Å °-0.00698439814453 Å °-0.0496834719511 Å °-0.0524172779613 Å °0.0144511642011 Å °
Refinement TLS groupSelection details: all

+
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