[English] 日本語
Yorodumi
- PDB-6h48: A polyamorous repressor: deciphering the evolutionary strategy us... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h48
TitleA polyamorous repressor: deciphering the evolutionary strategy used by the phage-inducible chromosomal islands to spread in nature.
ComponentsOrf20
KeywordsSTRUCTURAL PROTEIN / SaPI / repressor
Function / homologyHelix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / XRE family transcriptional regulator / Orf20
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsCiges-Tomas, J.R. / Alite, C. / Bowring, J.Z. / Donderis, J. / Penades, J.R. / Marina, A.
Funding support Spain, United Kingdom, 6items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Spanish Ministry of Economy and CompetitivenessFPU13/02880 Spain
Spanish Ministry of Economy and CompetitivenessBES-2014-068617 Spain
Medical Research Council (United Kingdom)MR/M003876/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N002873/1 United Kingdom
European Research CouncilERC-ADG-2014 670932 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature.
Authors: Rafael Ciges-Tomas, J. / Alite, C. / Humphrey, S. / Donderis, J. / Bowring, J. / Salvatella, X. / Penades, J.R. / Marina, A.
History
DepositionJul 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Orf20


Theoretical massNumber of molelcules
Total (without water)11,5821
Polymers11,5821
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.357, 77.357, 37.318
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein Orf20 / Stl


Mass: 11582.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F0J8, UniProt: A0A2S6DEV9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 40%PEG3350 0.1M Bis-Tris 0.2M Na-thiocyanate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.2→66.993 Å / Num. obs: 6522 / % possible obs: 96.7 % / Redundancy: 18.4 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.116 / Rsym value: 0.112 / Net I/av σ(I): 3.5 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.2-2.3216.71.0550.78430.2531.0861.05588.3
2.32-2.4619.70.6831.19130.1570.7010.683100
2.46-2.6319.50.461.68610.1060.4720.46100
2.63-2.8417.20.2682.47580.0640.2760.26892.3
2.84-3.1119.20.1923.17440.0450.1980.192100
3.11-3.4819.10.1413.96810.0330.1450.141100
3.48-4.0217.80.1135.15520.0270.1160.11392.6
4.02-4.9218.40.08475120.020.0860.084100
4.92-6.9617.60.0886.74150.0210.0910.088100
6.96-38.67916.60.0677.12430.0170.0690.06799.6

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→66.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.2484 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.198
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 292 4.5 %RANDOM
Rwork0.2484 ---
obs0.2491 6227 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.85 Å2 / Biso mean: 67.634 Å2 / Biso min: 31.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----2.45 Å2
Refinement stepCycle: final / Resolution: 2.2→66.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms665 0 0 19 684
Biso mean---67.9 -
Num. residues----77
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019676
X-RAY DIFFRACTIONr_bond_other_d00.02677
X-RAY DIFFRACTIONr_angle_refined_deg1.0022.018902
X-RAY DIFFRACTIONr_angle_other_deg3.21531573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1925.19776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75925.15233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67415145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.133153
X-RAY DIFFRACTIONr_chiral_restr0.0430.298
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02709
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02136
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 22 -
Rwork0.376 338 -
all-360 -
obs--76.27 %

+
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