[English] 日本語
Yorodumi
- PDB-2yfa: X-ray structure of McpS ligand binding domain in complex with malate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yfa
TitleX-ray structure of McpS ligand binding domain in complex with malate
ComponentsMETHYL-ACCEPTING CHEMOTAXIS TRANSDUCER
KeywordsRECEPTOR / CHEMORECEPTOR / CHEMOTAXIS
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
de novo design (two linked rop proteins) - #210 / Helical bimodular sensor domain / Helical bimodular sensor domain / HBM domain profile. / helical bimodular (HBM) domain / Chemotaxis methyl-accepting receptor / de novo design (two linked rop proteins) / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. ...de novo design (two linked rop proteins) - #210 / Helical bimodular sensor domain / Helical bimodular sensor domain / HBM domain profile. / helical bimodular (HBM) domain / Chemotaxis methyl-accepting receptor / de novo design (two linked rop proteins) / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / (2S)-2-hydroxybutanedioic acid / Methyl-accepting chemotaxis protein McpS
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsPineda-Molina, E. / Gavira, J.A. / Krell, T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Evidence for Chemoreceptors with Bimodular Ligand-Binding Regions Harboring Two Signal-Binding Sites.
Authors: Pineda-Molina, E. / Reyes-Darias, J. / Lacal, J. / Ramos, J.L. / Garcia-Ruiz, J.M. / Gavira, J.A. / Krell, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and Crystallographic Analysis of the Ligand-Binding Domain of the Pseudomonas Putida Chemoreceptor Mcps in Complex with Malate and Succinate.
Authors: Gavira, J.A. / Lacal, J. / Ramos, J.L. / Garcia-Ruiz, J.M. / Krell, T. / Pineda-Molina, E.
History
DepositionApr 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METHYL-ACCEPTING CHEMOTAXIS TRANSDUCER
B: METHYL-ACCEPTING CHEMOTAXIS TRANSDUCER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,02511
Polymers57,3042
Non-polymers7209
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-50.4 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.350, 45.850, 51.180
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein METHYL-ACCEPTING CHEMOTAXIS TRANSDUCER / MCPS


Mass: 28652.125 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 46-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: KT2440 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88E10

-
Non-polymers , 5 types, 542 molecules

#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.6 Å3/Da / Density % sol: 53.4 % / Description: NONE
Crystal growpH: 4.8
Details: 20% PEG 4000, 0.25 M (NH4)2SO4 AND 100 MM SODIUM ACETATE, PH 4.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.8→24.3 Å / Num. obs: 47287 / % possible obs: 96.8 % / Observed criterion σ(I): 1.99 / Redundancy: 3.79 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.96
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.49 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→24.308 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 2383 5 %
Rwork0.2088 --
obs0.211 47278 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.816 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.5524 Å20 Å2-1.257 Å2
2---1.8127 Å20 Å2
3---1.2603 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 43 533 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063722
X-RAY DIFFRACTIONf_angle_d0.8845015
X-RAY DIFFRACTIONf_dihedral_angle_d15.9831401
X-RAY DIFFRACTIONf_chiral_restr0.057572
X-RAY DIFFRACTIONf_plane_restr0.003671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86430.33382250.27444401X-RAY DIFFRACTION95
1.8643-1.93890.29782480.23734344X-RAY DIFFRACTION96
1.9389-2.02710.27932250.22124477X-RAY DIFFRACTION96
2.0271-2.13390.26242240.2164448X-RAY DIFFRACTION96
2.1339-2.26760.25152280.20184459X-RAY DIFFRACTION97
2.2676-2.44250.25112380.2014526X-RAY DIFFRACTION97
2.4425-2.6880.25922520.20374498X-RAY DIFFRACTION98
2.688-3.07630.24492530.214514X-RAY DIFFRACTION98
3.0763-3.87330.2222660.18734550X-RAY DIFFRACTION98
3.8733-24.30990.23822240.20614678X-RAY DIFFRACTION97

+
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