[English] 日本語
Yorodumi
- PDB-5fq1: Structure of the cytoplasmic PAS domain of the Geobacillus thermo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fq1
TitleStructure of the cytoplasmic PAS domain of the Geobacillus thermodenitrificans histidine kinase CitA
ComponentsHISTIDINE KINASE
KeywordsTRANSFERASE / PAS DOMAIN / CITA / TRANSMEMBRANE SIGNALING
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. ...SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Histidine kinase
Similarity search - Component
Biological speciesGEOBACILLUS THERMODENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
AuthorsSchomburg, B. / Giller, K. / Becker, S.
CitationJournal: Nat. Methods / Year: 2017
Title: Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.
Authors: Weisenburger, S. / Boening, D. / Schomburg, B. / Giller, K. / Becker, S. / Griesinger, C. / Sandoghdar, V.
History
DepositionDec 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HISTIDINE KINASE
B: HISTIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5439
Polymers24,8902
Non-polymers6537
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-42.3 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.453, 74.036, 75.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HISTIDINE KINASE / / CITA


Mass: 12444.914 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC PAS DOMAIN, UNP RESIDUES 200-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS THERMODENITRIFICANS (bacteria)
Description: DSM466 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4IPE6, histidine kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL GS IS DUE TO CLONING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 4.7
Details: 0.4 M K2HPO4, 1.6 M NAH2PO4, 0.1 M PHOSPHATE-CITRATE, PH 4.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97929
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.905
11-H, L, K20.095
ReflectionResolution: 1.78→37.54 Å / Num. obs: 18999 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.34 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.78
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 6.14 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SADABSdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.76→37.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.658 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21647 913 4.8 %RANDOM
Rwork0.18501 ---
obs0.18645 18034 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.382 Å2
Baniso -1Baniso -2Baniso -3
1-11.66 Å20 Å20 Å2
2---10.72 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.76→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 39 51 1757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191761
X-RAY DIFFRACTIONr_bond_other_d0.0080.021738
X-RAY DIFFRACTIONr_angle_refined_deg2.1712.012394
X-RAY DIFFRACTIONr_angle_other_deg1.61933977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69225.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1741513
X-RAY DIFFRACTIONr_chiral_restr0.1170.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02365
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7842.687905
X-RAY DIFFRACTIONr_mcbond_other2.7812.685904
X-RAY DIFFRACTIONr_mcangle_it3.6794.0091136
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.153.224856
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.763→1.808 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 34 -
Rwork0.246 835 -
obs--60.64 %

+
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