[English] 日本語
Yorodumi
- PDB-1dvo: THE X-RAY CRYSTAL STRUCTURE OF FINO, A REPRESSOR OF BACTERIAL CON... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dvo
TitleTHE X-RAY CRYSTAL STRUCTURE OF FINO, A REPRESSOR OF BACTERIAL CONJUGATION
ComponentsFERTILITY INHIBITION PROTEIN O
KeywordsTRANSCRIPTION / Repressor / Bacterial Conjugation
Function / homology
Function and homology information


Fertility inhibition protein FinO, N-terminal / Fertility inhibition protein N terminal / Fertility Inhibition Protein O; Chain: A; Domain 1 / ProQ/FinO domain / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fertility inhibition protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsGhetu, A.F. / Gubbins, M.J. / Frost, L.S. / Glover, J.N.M.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the bacterial conjugation repressor finO.
Authors: Ghetu, A.F. / Gubbins, M.J. / Frost, L.S. / Glover, J.N.
History
DepositionJan 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FERTILITY INHIBITION PROTEIN O


Theoretical massNumber of molelcules
Total (without water)17,3741
Polymers17,3741
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.570, 38.726, 145.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein FERTILITY INHIBITION PROTEIN O / FINO


Mass: 17374.115 Da / Num. of mol.: 1 / Mutation: L124M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / References: UniProt: P29367
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MES, Tris, EDTA, BME, NaCl, PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2150 mM1dropNaCl
350 mMMES1drop
40.1 %(v/v)beta-mercaptoethanol1drop
51 mMEDTA1drop
612 %PEG40001reservoir
750 mMTris-HCl1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X12C10.979
SYNCHROTRONAPS 14-BM-D20.9574
Detector
TypeIDDetector
BRANDEIS - B11CCD
ADSC QUANTUM 42CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.95741
ReflectionResolution: 2→20 Å / Num. all: 109290 / Num. obs: 14726 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.767 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.109 / Num. unique all: 853 / % possible all: 87
Reflection shell
*PLUS
% possible obs: 87 %

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.224 1475 -
Rwork0.197 --
all-14726 -
obs-14726 97.3 %
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 209 1428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_torsion_deg0.009
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.1 Å2
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.009
LS refinement shell
*PLUS
Rfactor Rfree: 0.234 / Rfactor Rwork: 0.204

+
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