[English] 日本語
Yorodumi
- PDB-1ffs: CHEY-BINDING DOMAIN OF CHEA IN COMPLEX WITH CHEY FROM CRYSTALS SO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ffs
TitleCHEY-BINDING DOMAIN OF CHEA IN COMPLEX WITH CHEY FROM CRYSTALS SOAKED IN ACETYL PHOSPHATE
Components
  • CHEMOTAXIS PROTEIN CHEA
  • CHEMOTAXIS PROTEIN CHEY
KeywordsTRANSFERASE/SIGNALING PROTEIN / doubly wound (beta/alpha)5 fold / TRANSFERASE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / bacterial-type flagellum ...negative regulation of protein modification process / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / bacterial-type flagellum / histidine phosphotransfer kinase activity / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / protein acetylation / histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / acetyltransferase activity / establishment of localization in cell / chemotaxis / phosphorylation / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CheY-binding domain of CheA / CheY binding / CheY binding / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain ...CheY-binding domain of CheA / CheY binding / CheY binding / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chemotaxis protein CheY / Chemotaxis protein CheA / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGouet, P. / Chinardet, N. / Welch, M. / Guillet, V. / Birck, C. / Mourey, L. / Samama, J.-P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Further insights into the mechanism of function of the response regulator CheY from crystallographic studies of the CheY--CheA(124--257) complex.
Authors: Gouet, P. / Chinardet, N. / Welch, M. / Guillet, V. / Cabantous, S. / Birck, C. / Mourey, L. / Samama, J.P.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY.
Authors: WELCH, M. / CHINARDET, N. / MOUREY, L. / BIRCK, C. / SAMAMA, J.-P.
History
DepositionJul 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CHEMOTAXIS PROTEIN CHEY
B: CHEMOTAXIS PROTEIN CHEA
C: CHEMOTAXIS PROTEIN CHEY
D: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0316
Polymers56,9214
Non-polymers1102
Water4,306239
1
A: CHEMOTAXIS PROTEIN CHEY
B: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5153
Polymers28,4602
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CHEMOTAXIS PROTEIN CHEY
D: CHEMOTAXIS PROTEIN CHEA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5153
Polymers28,4602
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.300, 53.400, 77.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CHEMOTAXIS PROTEIN CHEY


Mass: 13981.136 Da / Num. of mol.: 2 / Fragment: RESIDUES 124-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P06143, UniProt: P0AE67*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Protein CHEMOTAXIS PROTEIN CHEA


Mass: 14479.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P07363
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG MME 5K, 0.1 M MALONIC ACID, 0.1 M MES BUFFER 0.02 M DTT, 0.01 M MANGANESE CHLORIDE , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Details: Welch, M., (1998) Nature Struct. Biol., 5, 25.

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 63874 / Num. obs: 26184 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.2 / % possible all: 98
Reflection
*PLUS
Num. measured all: 63874
Reflection shell
*PLUS
% possible obs: 98.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.2

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 1772 RANDOM
Rwork0.217 --
all0.219 25738 -
obs0.219 25738 -
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 2 239 3223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_torsion_deg23.8
X-RAY DIFFRACTIONc_torsion_impr_deg1.6
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

+
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://pdbjlvh1.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