[English] 日本語
Yorodumi
- PDB-1f4v: CRYSTAL STRUCTURE OF ACTIVATED CHEY BOUND TO THE N-TERMINUS OF FLIM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f4v
TitleCRYSTAL STRUCTURE OF ACTIVATED CHEY BOUND TO THE N-TERMINUS OF FLIM
Components
  • CHEMOTAXIS CHEY PROTEIN
  • FLAGELLAR MOTOR SWITCH PROTEIN
KeywordsSIGNALING PROTEIN / response regulator / peptide-protein complex / bacterial signal transduction / BeF3
Function / homology
Function and homology information


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 / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation ...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 / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / positive chemotaxis / protein acetylation / acetyltransferase activity / cytoskeletal motor activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / CheC-like superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / CheC-like superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Chemotaxis protein CheY / Flagellar motor switch protein FliM / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.22 Å
AuthorsLee, S.Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Henderson, R.K. / King, D. / Huang, L.S. / Kustu, S. / Berry, E.A. / Wemmer, D.E.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of an activated response regulator bound to its target.
Authors: Lee, S.Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Henderson, R.K. / King, D.S. / Huang, L. / Kustu, S. / Berry, E.A. / Wemmer, D.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Beryllofluoride Mimics Phosphorylation of NtrC and other Bacterial Response Regulators
Authors: Yan, D. / Cho, H.S. / Hastings, C.A. / Igo, M.M. / Lee, S.Y. / Pelton, J.G. / Stewart, V. / Wemmer, D.E. / Kustu, S.
#3: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structure of Escherichia coli CheY Refined at 1.7-A Resolution
Authors: Volz, K. / Matsumura, P.
History
DepositionJun 10, 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: Non-polymer description / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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 CHEY PROTEIN
B: CHEMOTAXIS CHEY PROTEIN
C: CHEMOTAXIS CHEY PROTEIN
D: FLAGELLAR MOTOR SWITCH PROTEIN
E: FLAGELLAR MOTOR SWITCH PROTEIN
F: FLAGELLAR MOTOR SWITCH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,46814
Polymers47,0136
Non-polymers4558
Water5,044280
1
A: CHEMOTAXIS CHEY PROTEIN
D: FLAGELLAR MOTOR SWITCH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8535
Polymers15,6712
Non-polymers1823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-13 kcal/mol
Surface area7470 Å2
MethodPISA
2
B: CHEMOTAXIS CHEY PROTEIN
E: FLAGELLAR MOTOR SWITCH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8535
Polymers15,6712
Non-polymers1823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-11 kcal/mol
Surface area6970 Å2
MethodPISA
3
C: CHEMOTAXIS CHEY PROTEIN
F: FLAGELLAR MOTOR SWITCH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7614
Polymers15,6712
Non-polymers902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.232, 54.233, 347.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules ABCDEF

#1: Protein CHEMOTAXIS CHEY PROTEIN


Mass: 13981.136 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Protein/peptide FLAGELLAR MOTOR SWITCH PROTEIN / / FLIM


Mass: 1689.884 Da / Num. of mol.: 3 / Fragment: N-TERMINUS / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P06974

-
Non-polymers , 4 types, 288 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: ammonium sulfate, glycerol, Tris, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6 Mammonium sulfate1reservoir
210 %(v/v)glycerol1reservoir
3100 mMTris1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.211.2
SYNCHROTRONSSRL BL1-520.9799
SYNCHROTRONSSRL BL1-530.9796
SYNCHROTRONSSRL BL1-540.9253
Detector
TypeIDDetectorDate
ADSC QUANTUM 41IMAGE PLATEOct 15, 1999
FUJI2IMAGE PLATEJan 6, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
20.97991
30.97961
40.92531
ReflectionResolution: 2.2→24.7 Å / Num. all: 121390 / Num. obs: 28982 / % possible obs: 92.9 % / Observed criterion σ(F): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.318 / Num. unique all: 1314 / % possible all: 84.7
Reflection
*PLUS
Num. measured all: 121390 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 84.7 %

-
Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.22→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1216673.62 / Data cutoff high rms absF: 1216673.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1442 5 %RANDOM
Rwork0.217 ---
all0.2189 28857 --
obs0.2189 28623 93 %-
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å21.96 Å20 Å2
2---0.04 Å20 Å2
3---0.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 27 280 3553
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it3.331.5
X-RAY DIFFRACTIONc_mcangle_it4.712
X-RAY DIFFRACTIONc_scbond_it5.272
X-RAY DIFFRACTIONc_scangle_it7.052.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.22→2.36 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 231 5.3 %
Rwork0.316 4087 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2GOL_PAR
X-RAY DIFFRACTION3SO4_PAR
X-RAY DIFFRACTION4PARAM19.RCV
X-RAY DIFFRACTION5WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.376 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.316

+
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