[English] 日本語
Yorodumi
- PDB-7prr: Structure of the ligand binding domain of the PctD (PA4633) chemo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7prr
TitleStructure of the ligand binding domain of the PctD (PA4633) chemoreceptor of Pseudomonas aeruginosa PAO1 in complex with acetylcholine
ComponentsProbable chemotaxis transducer
KeywordsSIGNALING PROTEIN / Ligand binding domain / Pseudomonas aeruginosa / chemotactic transducer
Function / homology
Function and homology information


chemotaxis / signal transduction / metal ion binding / plasma membrane
Similarity search - Function
Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS domain / Beta-Lactamase ...Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYLCHOLINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Probable chemotaxis transducer
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGavira, J.A. / Matilla, M.A. / Martin-Mora, D. / Krell, T.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-74875-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2016-76779-P Spain
CitationJournal: Mbio / Year: 2022
Title: Chemotaxis of the Human Pathogen Pseudomonas aeruginosa to the Neurotransmitter Acetylcholine.
Authors: Matilla, M.A. / Velando, F. / Tajuelo, A. / Martin-Mora, D. / Xu, W. / Sourjik, V. / Gavira, J.A. / Krell, T.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable chemotaxis transducer
B: Probable chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,94610
Polymers76,9062
Non-polymers1,0398
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint26 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.288, 102.650, 104.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Probable chemotaxis transducer


Mass: 38453.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ligand binding domain
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4633 / Plasmid: PET28B+
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HVF8

-
Non-polymers , 5 types, 460 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 4.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→47.48 Å / Num. obs: 62249 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.043 / Rrim(I) all: 0.096 / Net I/σ(I): 10.7 / Num. measured all: 280823 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.844.51.0171671036950.5810.5151.1471.299.7
9-47.484.30.02224145560.9980.0110.02442.895.5

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19-4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PRQ

7prq


Resolution: 1.8→47.48 Å / SU ML: 0.2018 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207 3166 5.09 %
Rwork0.1668 58994 -
obs0.1689 62160 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 68 452 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215184
X-RAY DIFFRACTIONf_angle_d1.09067062
X-RAY DIFFRACTIONf_chiral_restr0.0624762
X-RAY DIFFRACTIONf_plane_restr0.0088950
X-RAY DIFFRACTIONf_dihedral_angle_d16.1222013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.32031270.28892558X-RAY DIFFRACTION99.48
1.83-1.860.29331210.28062575X-RAY DIFFRACTION99.59
1.86-1.890.32311350.25732549X-RAY DIFFRACTION99.11
1.89-1.920.31081330.25032543X-RAY DIFFRACTION99.33
1.92-1.950.29641280.24452554X-RAY DIFFRACTION99.19
1.95-1.990.2481510.22332559X-RAY DIFFRACTION99.67
1.99-2.030.24451440.21652543X-RAY DIFFRACTION99.15
2.03-2.080.29691230.20372548X-RAY DIFFRACTION98.78
2.08-2.120.24151260.19022578X-RAY DIFFRACTION99.45
2.12-2.180.21561560.17322541X-RAY DIFFRACTION99.48
2.18-2.240.21851460.16952567X-RAY DIFFRACTION99.34
2.24-2.30.23341460.16352561X-RAY DIFFRACTION99.49
2.3-2.380.20841290.16062572X-RAY DIFFRACTION99.16
2.38-2.460.20811270.15512567X-RAY DIFFRACTION99.59
2.46-2.560.24061400.15612576X-RAY DIFFRACTION99.09
2.56-2.680.19941330.16162568X-RAY DIFFRACTION98.68
2.68-2.820.21221500.15212556X-RAY DIFFRACTION98.76
2.82-2.990.17481600.15512556X-RAY DIFFRACTION98.26
2.99-3.220.22211570.16512537X-RAY DIFFRACTION98.11
3.22-3.550.17861220.15042571X-RAY DIFFRACTION97.36
3.55-4.060.15491180.13832588X-RAY DIFFRACTION96.89
4.06-5.120.15481420.12672575X-RAY DIFFRACTION96.25
5.12-47.480.21661520.17992652X-RAY DIFFRACTION94.73

+
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