[English] 日本語
Yorodumi
- PDB-9fku: Crystal Structure of AimR from Katmira phage -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fku
TitleCrystal Structure of AimR from Katmira phage
Components
  • Arbitrium receptor
  • GLY-VAL-VAL-ARG-GLY-ALA
KeywordsDNA BINDING PROTEIN / Arbitrium receptor
Function / homology: / AimR transcriptional regulator-like / ACETATE ION / Arbitrium receptor
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGallego del Sol, F. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
CitationJournal: To Be Published
Title: Crystal Structure of AimR from Katmira phage
Authors: Gallego del Sol, F. / Marina, A.
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arbitrium receptor
B: Arbitrium receptor
C: GLY-VAL-VAL-ARG-GLY-ALA
D: GLY-VAL-VAL-ARG-GLY-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,17310
Polymers91,6414
Non-polymers5326
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-44 kcal/mol
Surface area34600 Å2
Unit cell
Length a, b, c (Å)69.765, 203.582, 143.069
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-620-

HOH

21B-696-

HOH

-
Components

#1: Protein Arbitrium receptor


Mass: 45261.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A8I3AZZ2
#2: Protein/peptide GLY-VAL-VAL-ARG-GLY-ALA


Mass: 558.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 15% pentaeritritol ethoxilate, 3% jeffamine, 0.2M Potassium Acetate, 0.1M MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→48.64 Å / Num. obs: 80454 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7816 / CC1/2: 0.664 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21206 4067 -RANDOM
Rwork0.17829 ---
obs0.17999 76351 99.96 %-
Displacement parametersBiso mean: 40.967 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0.12 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 0 36 396 6864
LS refinement shellResolution: 1.9→1.949 Å /
Rfactor% reflection
Rfree0.326 -
Rwork0.321 -
obs-99.98 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0053-0.036-0.21721.31430.2531.6087-0.06140.22490.11230.22490.0859-0.01990.1123-0.0199-0.02450.04760.0225-0.02490.051-0.03010.022222.859843.485910.4793
20.95060.0413-0.44421.0290.28011.6182-0.0490.07940.08720.07940.0303-0.03970.0872-0.03970.01870.0978-0.0173-0.0130.02010.01880.0702-9.2317.3942.22
35.621-2.6558-6.30373.59322.48497.1835-0.3061-0.04040.4182-0.04040.11270.08430.41820.08430.19340.1296-0.01370.01510.059-0.0290.076925.598741.3291.4206
40.37130.1965-0.11742.5374-2.30956.05990.0937-0.0426-0.237-0.04260.05470.16-0.2370.16-0.14840.0935-0.02220.01180.0466-0.00150.1108-5.840917.8081-6.8504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 386
2X-RAY DIFFRACTION2B1 - 386
3X-RAY DIFFRACTION3C1 - 6
4X-RAY DIFFRACTION4D1 - 6

+
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