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- PDB-1f4v: CRYSTAL STRUCTURE OF ACTIVATED CHEY BOUND TO THE N-TERMINUS OF FLIM -

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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 / internal peptidyl-lysine acetylation / regulation of chemotaxis / thermotaxis / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum ...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 / internal peptidyl-lysine acetylation / regulation of chemotaxis / thermotaxis / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / phosphorelay response regulator activity / protein acetylation / positive chemotaxis / acetyltransferase activity / phosphorelay signal transduction system / cytoskeletal motor activity / chemotaxis / magnesium ion binding / signal transduction / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / : / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / : / 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.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: NMR Structure of Activated CheY
Authors: Cho, H.S. / Lee, S.Y. / Yan, D. / Pan, X. / Parkinson, J.S. / Kustu, S. / Wemmer, D.E. / Pelton, J.G.
#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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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


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


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

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Experimental details

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Experiment

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

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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

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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 %

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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

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