[English] 日本語
Yorodumi
- PDB-5ubd: Crystal structure of the N-terminal domain (domain 1) of RctB, Rc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ubd
TitleCrystal structure of the N-terminal domain (domain 1) of RctB, RctB-1-124-L48M
ComponentsRctB replication initiator protein
KeywordsDNA BINDING PROTEIN / DNA replication initiation / DNA binding / secondary chromosome / Vibrio cholerae
Function / homologyReplication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / DUF3346 domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsOrlova, N. / Ivashkiv, O. / Waldor, M.K. / Jeruzalmi, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM084162 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators.
Authors: Orlova, N. / Gerding, M. / Ivashkiv, O. / Olinares, P.D.B. / Chait, B.T. / Waldor, M.K. / Jeruzalmi, D.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RctB replication initiator protein
B: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)29,9982
Polymers29,9982
Non-polymers00
Water2,738152
1
A: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)14,9991
Polymers14,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RctB replication initiator protein


Theoretical massNumber of molelcules
Total (without water)14,9991
Polymers14,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.451, 38.167, 63.042
Angle α, β, γ (deg.)97.46, 91.49, 98.43
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein RctB replication initiator protein


Mass: 14998.834 Da / Num. of mol.: 2 / Fragment: domain 1 (UNP residues 1-124) / Mutation: L48M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: DN30_18, EN12_14105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085QGR2, UniProt: Q9KNG2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.58 Å3/Da / Density % sol: 52.41 % / Description: plate
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystals of selenomethionine-substituted RctB domain 1 (1 - 124, L48M) were grown by mixing 0.1, or 0.2, or 0.4 uL of the protein solution (20.1 mg/ml RctB-2-124-L48M in 20 mM Tris pH 7.4, ...Details: Crystals of selenomethionine-substituted RctB domain 1 (1 - 124, L48M) were grown by mixing 0.1, or 0.2, or 0.4 uL of the protein solution (20.1 mg/ml RctB-2-124-L48M in 20 mM Tris pH 7.4, 500 mM sodium chloride, 5% glycerol, 5 mM 2-mercaptoethanol) and 0.2 uL of reservoir solution (0.1 M Sodium HEPES pH 7.5, 20% w/v PEG10000).
Temp details: cold room

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen cryo stream
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19914 / % possible obs: 94.3 % / Redundancy: 2 % / Rsym value: 0.049 / Net I/σ(I): 26.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.44 / CC1/2: 0.712 / Rsym value: 0.496 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
HKL-2000v714data reduction
HKL-2000v714data scaling
AutoSol1.11-2567-000phasing
PHENIX1.11-2567-000model building
RefinementMethod to determine structure: SAD / Resolution: 2.002→34.191 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 31.58
RfactorNum. reflection% reflection
Rfree0.247 1818 10.01 %
Rwork0.2138 --
obs0.2171 18162 91.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→34.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 152 1998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031874
X-RAY DIFFRACTIONf_angle_d0.5812524
X-RAY DIFFRACTIONf_dihedral_angle_d10.7031142
X-RAY DIFFRACTIONf_chiral_restr0.04294
X-RAY DIFFRACTIONf_plane_restr0.003322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0025-2.05660.41311160.37041098X-RAY DIFFRACTION80
2.0566-2.11710.43151160.38071019X-RAY DIFFRACTION73
2.1171-2.18550.32691440.28061288X-RAY DIFFRACTION94
2.1855-2.26360.35541130.3191025X-RAY DIFFRACTION74
2.2636-2.35420.34461390.26691214X-RAY DIFFRACTION88
2.3542-2.46130.30041470.24221324X-RAY DIFFRACTION96
2.4613-2.5910.26711470.24111317X-RAY DIFFRACTION96
2.591-2.75330.28931510.24941334X-RAY DIFFRACTION95
2.7533-2.96570.30471500.23331360X-RAY DIFFRACTION98
2.9657-3.2640.25491500.23261347X-RAY DIFFRACTION98
3.264-3.73580.24581500.20661340X-RAY DIFFRACTION97
3.7358-4.70470.17151500.16131363X-RAY DIFFRACTION98
4.7047-34.19620.18811450.1671315X-RAY DIFFRACTION96

+
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://pdbjlvh1.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