[English] 日本語
Yorodumi
- PDB-3a0s: PAS domain of histidine kinase ThkA (TM1359) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a0s
TitlePAS domain of histidine kinase ThkA (TM1359)
ComponentsSensor protein
KeywordsTRANSFERASE / PAS-fold / Kinase / Phosphoprotein / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain ...His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 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 / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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: Advisory / Version format compliance
Revision 1.2Aug 17, 2011Group: Data collection
Revision 1.3Nov 1, 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2537
Polymers11,2201
Non-polymers1,0336
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.784, 43.784, 115.448
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Sensor protein / / Histidine kinase ThkA


Mass: 11219.812 Da / Num. of mol.: 1 / Fragment: PAS 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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 50% PEG200, 0.1M sodium/potassium-phosphate pH 6.2, 0.2M sodium chloride, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2007
RadiationMonochromator: Si 111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→30 Å / Num. obs: 19750 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 18.2 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.047 / Net I/σ(I): 41.5
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.334 / % possible all: 88.9

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A0V

3a0v


Resolution: 1.47→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.51 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 967 4.9 %RANDOM
Rwork0.21 ---
obs0.211 19680 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.41 Å2 / Biso mean: 27.384 Å2 / Biso min: 11.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.47→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms793 0 69 50 912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022901
X-RAY DIFFRACTIONr_angle_refined_deg1.5222.0221183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.024595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90723.91346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5215167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.113158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02629
X-RAY DIFFRACTIONr_nbd_refined0.2290.2387
X-RAY DIFFRACTIONr_nbtor_refined0.310.2602
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.221
X-RAY DIFFRACTIONr_mcbond_it1.0551.5498
X-RAY DIFFRACTIONr_mcangle_it1.5932790
X-RAY DIFFRACTIONr_scbond_it2.6913442
X-RAY DIFFRACTIONr_scangle_it3.9554.5393
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 65 -
Rwork0.255 1197 -
all-1262 -
obs--87.52 %
Refinement TLS params.Method: refined / Origin x: 8.758 Å / Origin y: 5.128 Å / Origin z: 42.929 Å
111213212223313233
T-0.0879 Å2-0.0062 Å2-0.0056 Å2--0.021 Å2-0.0033 Å2---0.0755 Å2
L0.7741 °20.1065 °2-0.2412 °2-0.3742 °2-0.2945 °2--1.9226 °2
S0.0224 Å °0.0758 Å °0.0461 Å °-0.0407 Å °-0.0099 Å °0.0163 Å °0.1964 Å °-0.0777 Å °-0.0125 Å °

+
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