[English] 日本語
Yorodumi
- PDB-7k5n: Ligand binding domain (tandem PAS/dCache) of Aeromonas caviae dig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k5n
TitleLigand binding domain (tandem PAS/dCache) of Aeromonas caviae diguanylate cyclase with proline bound
ComponentsSensor domain-containing diguanylate cyclase
KeywordsSIGNALING PROTEIN / PAS / Cache / bacterial inner membrane bound / amino acid binder
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / : / Periplasmic sensor-like domain superfamily / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
PROLINE / diguanylate cyclase
Similarity search - Component
Biological speciesAeromonas caviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSweeney, E.G. / Remington, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM125576 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01HD22486 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)5F32DK108591-03 United States
CitationJournal: Cell Host Microbe / Year: 2021
Title: Host-emitted amino acid cues regulate bacterial chemokinesis to enhance colonization.
Authors: Robinson, C.D. / Sweeney, E.G. / Ngo, J. / Ma, E. / Perkins, A. / Smith, T.J. / Fernandez, N.L. / Waters, C.M. / Remington, S.J. / Bohannan, B.J.M. / Guillemin, K.
History
DepositionSep 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensor domain-containing diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6643
Polymers31,4571
Non-polymers2072
Water54030
1
A: Sensor domain-containing diguanylate cyclase
hetero molecules

A: Sensor domain-containing diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3286
Polymers62,9132
Non-polymers4144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+1,y,-z+11
Buried area2800 Å2
ΔGint-12 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.188, 86.188, 75.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein Sensor domain-containing diguanylate cyclase


Mass: 31456.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: zebrafish isolate Guillemin lab, ZOR0002 / Source: (gene. exp.) Aeromonas caviae (bacteria) / Gene: C0708_15830, C1C92_04435 / Plasmid: pBH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3S5WQC2
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: crystal growth conditions: 80 mM sodium acetate trihydrate pH 4.5 and 1.4 - 1.5 M sodium formate. cryoprotectant was the crystal growth conditions plus 10 mM proline and 20% glycerol. ...Details: crystal growth conditions: 80 mM sodium acetate trihydrate pH 4.5 and 1.4 - 1.5 M sodium formate. cryoprotectant was the crystal growth conditions plus 10 mM proline and 20% glycerol. crystals were briefly (< 1min) swished through cryoprotectant before flash frozen in liquid nitrogen
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: collected under cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26946 / % possible obs: 99.99 % / Redundancy: 20 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.064 / Rrim(I) all: 0.089 / Net I/σ(I): 30
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1304 / CC1/2: 0.208 / CC star: 0.586

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c8c

3c8c


Resolution: 1.8→30.47 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 39.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2607 1332 5 %
Rwork0.2362 25331 -
obs0.2375 26663 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.91 Å2 / Biso mean: 62.9754 Å2 / Biso min: 35.5 Å2
Refinement stepCycle: final / Resolution: 1.8→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 26 30 1945
Biso mean--55.17 54.49 -
Num. residues----237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.54471230.49542359248294
1.86-1.940.49491300.47512432256297
1.94-2.020.34631310.33212485261699
2.02-2.130.36381320.308725222654100
2.13-2.260.38891340.301625292663100
2.26-2.440.29051340.255825392673100
2.44-2.680.32271320.26225472679100
2.68-3.070.29081350.259525582693100
3.07-3.870.24761380.222326062744100
3.87-30.470.21221430.200227542897100

+
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