[English] 日本語
Yorodumi
- PDB-3a0w: Catalytic domain of histidine kinase ThkA (TM1359) for MAD phasin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a0w
TitleCatalytic domain of histidine kinase ThkA (TM1359) for MAD phasing (nucleotide free form 2, orthorombic)
ComponentsSensor protein
KeywordsTRANSFERASE / ATP-lid / Kinase / Phosphoprotein / Two-component regulatory system
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / regulation of DNA-templated transcription / signal transduction / ATP binding / metal ion binding
Similarity search - Function
His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase/HSP90-like ATPase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHYL MERCURY ION / 2-(ETHYLMERCURI-THIO)-BENZOIC ACID / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.69 Å
AuthorsYamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
CitationJournal: Structure / Year: 2009
Title: Structure of PAS-linked histidine kinase and the response regulator complex
Authors: Yamada, S. / Sugimoto, H. / Kobayashi, M. / Ohno, A. / Nakamura, H. / Shiro, Y.
History
DepositionMar 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Sensor protein
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9909
Polymers35,4522
Non-polymers1,5387
Water4,179232
1
A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6875
Polymers17,7261
Non-polymers9604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3044
Polymers17,7261
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.092, 61.148, 90.287
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sensor protein / Histidine kinase ThkA


Mass: 17726.236 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1359 / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q9X180, histidine kinase
#2: Chemical
ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Chemical ChemComp-EMT / 2-(ETHYLMERCURI-THIO)-BENZOIC ACID


Mass: 382.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10HgO2S
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 40% MPD, 0.1M sodium cacodylate, 5% PEG8000, pH 6.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.0072, 1.0090, 0.9900
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 30, 2006
RadiationMonochromator: Si 111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00721
21.0091
30.991
ReflectionResolution: 1.69→20 Å / Num. obs: 36504 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.069 / Net I/σ(I): 25.4
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.305 / % possible all: 93

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
SPACEdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.69→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.286 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1832 5 %RANDOM
Rwork0.213 ---
obs0.214 36456 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.86 Å2 / Biso mean: 23.063 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.69→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 47 232 2778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222594
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9793483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29324.697132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14615508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.651520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021920
X-RAY DIFFRACTIONr_nbd_refined0.2120.21236
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.216
X-RAY DIFFRACTIONr_mcbond_it1.1721.51567
X-RAY DIFFRACTIONr_mcangle_it1.84922479
X-RAY DIFFRACTIONr_scbond_it2.69831159
X-RAY DIFFRACTIONr_scangle_it4.0354.5997
LS refinement shellResolution: 1.688→1.732 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 103 -
Rwork0.294 2421 -
all-2524 -
obs--93.52 %

+
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