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- PDB-2fmh: Crystal structure of Mg2+ and BeF3- bound CheY in complex with Ch... -

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Basic information

Entry
Database: PDB / ID: 2fmh
TitleCrystal structure of Mg2+ and BeF3- bound CheY in complex with CheZ 200-214 solved from a F432 crystal grown in Tris (pH 8.4)
Components
  • C-terminal 15-mer from Chemotaxis protein cheZ
  • Chemotaxis protein cheY
KeywordsSIGNALING PROTEIN / CHEMOTAXIS / BEF(3)(-)-BOUND CHEY / CHEY-CHEZ PEPTIDE COMPLEX
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of chemotaxis / bacterial-type flagellum / phosphorelay signal transduction system / phosphoprotein phosphatase activity / chemotaxis / metal ion binding / cytoplasm
Similarity search - Function
Chemotaxis phosphatase, CheZ / Chemotaxis phosphatase, CheZ / : / : / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator ...Chemotaxis phosphatase, CheZ / Chemotaxis phosphatase, CheZ / : / : / 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 / Protein phosphatase CheZ / Chemotaxis protein CheY
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsGuhaniyogi, J. / Robinson, V.L. / Stock, A.M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Beryllium Fluoride-free and Beryllium Fluoride-bound CheY in Complex with the Conserved C-terminal Peptide of CheZ Reveal Dual Binding Modes Specific to CheY Conformation.
Authors: Guhaniyogi, J. / Robinson, V.L. / Stock, A.M.
History
DepositionJan 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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.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_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_ref_seq_dif.details / _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 protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1647
Polymers15,7632
Non-polymers4015
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-14 kcal/mol
Surface area7250 Å2
MethodPISA
2
A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)387,928168
Polymers378,31448
Non-polymers9,615120
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation57_554y+1/2,z,x-1/21
crystal symmetry operation59_555y+1/2,-z,-x+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation60_554-y+1/2,-z,x-1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
crystal symmetry operation71_554-z+1/2,y,x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation69_555z+1/2,y,-x+1/21
crystal symmetry operation77_545z+1/2,x-1/2,y1
crystal symmetry operation78_555z+1/2,-x+1/2,-y1
crystal symmetry operation80_545-z+1/2,x-1/2,-y1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation86_555-y+1/2,-x+1/2,-z1
crystal symmetry operation88_545-y+1/2,x-1/2,z1
crystal symmetry operation87_555y+1/2,-x+1/2,z1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
Buried area67570 Å2
ΔGint-1014 kcal/mol
Surface area137820 Å2
MethodPISA
3
A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules

A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules

A: Chemotaxis protein cheY
B: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,49121
Polymers47,2896
Non-polymers1,20215
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
Buried area7570 Å2
ΔGint-114 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.802, 197.802, 197.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-154-

SO4

21A-150-

TRS

31A-150-

TRS

41A-9047-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Chemotaxis protein cheY


Mass: 14140.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: cheY / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P0A2D5
#2: Protein/peptide C-terminal 15-mer from Chemotaxis protein cheZ


Mass: 1622.687 Da / Num. of mol.: 1 / Fragment: residues 200-214 / Source method: obtained synthetically
Details: This sequence corresponds to the C-terminal 15 residues of the CheZ protein occurring naturally in Salmonella enterica serovar Typhumurium
References: UniProt: P07800

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Non-polymers , 6 types, 58 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 2M ammonium sulfate, 0.2M lithium sulfate, 0.1M Tris, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0718 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004
RadiationMonochromator: KOHZU double crystal monochromator with a sagittally focused second crystal. Crystal type Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionNumber: 22923 / Rmerge(I) obs: 0.068 / Χ2: 1.065 / D res high: 2 Å / D res low: 30 Å / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.313099.410.0450.957
3.424.3110010.0480.991
2.993.4210010.0610.968
2.712.9910010.0831.091
2.522.7110010.1091.05
2.372.5210010.1441.047
2.252.3710010.1751.112
2.152.2510010.231.131
2.072.1510010.2941.16
22.0710010.3771.164
ReflectionResolution: 2→30 Å / Num. all: 22957 / Num. obs: 22923 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.068 / Χ2: 1.065 / Net I/σ(I): 35.7
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 7 / Num. unique all: 2207 / Rsym value: 0.377 / Χ2: 1.164 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FQW

1fqw


Resolution: 2.001→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.601 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24636 2330 10.2 %RANDOM
Rwork0.21991 ---
all0.223 22939 --
obs0.2253 22923 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.762 Å2
Refinement stepCycle: LAST / Resolution: 2.001→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 24 53 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221191
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9971603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2895145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.4526.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24415232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.813154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02858
X-RAY DIFFRACTIONr_nbd_refined0.2230.2526
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2794
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.258
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.211
X-RAY DIFFRACTIONr_mcbond_it0.8781.5774
X-RAY DIFFRACTIONr_mcangle_it1.42121188
X-RAY DIFFRACTIONr_scbond_it2.1543475
X-RAY DIFFRACTIONr_scangle_it3.2414.5415
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 184 -
Rwork0.239 1466 -
obs-1650 100 %

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