[English] 日本語
Yorodumi
- PDB-2fmf: Crystal structure of CheY in complex with CheZ 200-214 solved fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fmf
TitleCrystal structure of CheY in complex with CheZ 200-214 solved from a F432 crystal grown in Hepes (pH 7.5)
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
Protein phosphatase CheZ / Chemotaxis protein CheY
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 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_special_symmetry / 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 / _struct_ref_seq_dif.details / _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: C-terminal 15-mer from Chemotaxis protein cheZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8593
Polymers15,7632
Non-polymers961
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.140, 197.140, 197.140
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-150-

SO4

21A-150-

SO4

31A-210-

HOH

-
Components

#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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 0.2M lithium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2003
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: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.998→20 Å / Num. all: 22840 / Num. obs: 22136 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 22
Reflection shellResolution: 1.998→2.07 Å / Mean I/σ(I) obs: 6.6 / Num. unique all: 2148 / Rsym value: 0.251 / % possible all: 97

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FQW

1fqw


Resolution: 1.998→19.8 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.483 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21319 2148 9.9 %RANDOM
Rwork0.20006 ---
all0.20134 22128 --
obs0.20134 21659 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.445 Å2
Refinement stepCycle: LAST / Resolution: 1.998→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 5 86 1175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221119
X-RAY DIFFRACTIONr_bond_other_d0.0010.021036
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9851504
X-RAY DIFFRACTIONr_angle_other_deg2.6532423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.953140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80315219
X-RAY DIFFRACTIONr_chiral_restr0.0930.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021236
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02207
X-RAY DIFFRACTIONr_nbd_refined0.2370.3249
X-RAY DIFFRACTIONr_nbd_other0.2080.3968
X-RAY DIFFRACTIONr_nbtor_other0.2430.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.598
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1680.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.770.524
X-RAY DIFFRACTIONr_mcbond_it0.7341.5703
X-RAY DIFFRACTIONr_mcangle_it1.41121122
X-RAY DIFFRACTIONr_scbond_it2.243416
X-RAY DIFFRACTIONr_scangle_it3.8854.5382
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 148 -
Rwork0.221 1369 -
obs-1517 97 %

+
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