[English] 日本語
Yorodumi
- PDB-4i5s: Structure and function of sensor histidine kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i5s
TitleStructure and function of sensor histidine kinase
ComponentsPutative histidine kinase CovS; VicK-like protein
KeywordsTRANSFERASE / HISTIDINE KINASE / VICK / HAMP / PAS / Kinase / Phosphorylation
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / regulation of DNA-templated transcription
Similarity search - Function
HAMP domain in histidine kinase / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) 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. ...HAMP domain in histidine kinase / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) 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. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Beta-Lactamase / PAS fold / PAS fold / Helicase, Ruva Protein; domain 3 / 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 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsCai, Y.
CitationJournal: Plos Biol. / Year: 2013
Title: Mechanistic insights revealed by the crystal structure of a histidine kinase with signal transducer and sensor domains
Authors: Wang, C. / Sang, J. / Wang, J. / Su, M. / Downey, J.S. / Wu, Q. / Wang, S. / Cai, Y. / Xu, X. / Wu, J. / Senadheera, D.B. / Cvitkovitch, D.G. / Chen, L. / Goodman, S.D. / Han, A.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative histidine kinase CovS; VicK-like protein
B: Putative histidine kinase CovS; VicK-like protein


Theoretical massNumber of molelcules
Total (without water)103,5042
Polymers103,5042
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-58 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.124, 153.124, 125.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Putative histidine kinase CovS; VicK-like protein / HAMP / HISTIDINE KINASE-LIKE ATPASES / PAS DOMAIN / HISTIDINE KINASE A DOMAIN


Mass: 51752.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans serotype c (bacteria)
Strain: ATCC 700610 / UA159 / Gene: covS, SMU_1516 / Plasmid: PCRT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 ROSETTA / References: UniProt: Q8DT64, EC: 2.7.13.1

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.3-2.9M SODIUM FORMATE, 3% PEG 4000, PH 7.6-8.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 7, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 25746 / % possible obs: 99.5 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 21.1 / Redundancy: 5.9 % / Biso Wilson estimate: 102 Å2
Reflection shellResolution: 3.3→3.42 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.3→36.62 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.93 / σ(F): 1.35 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1451 5.64 %RANDOM
Rwork0.23 ---
obs0.233 25719 99.6 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 125.53 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 276.76 Å2 / Biso mean: 151.3412 Å2 / Biso min: 78.04 Å2
Baniso -1Baniso -2Baniso -3
1-10.7354 Å20 Å2-0 Å2
2--10.7354 Å20 Å2
3----21.4708 Å2
Refinement stepCycle: LAST / Resolution: 3.3→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 0 0 6233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056312
X-RAY DIFFRACTIONf_angle_d0.9348530
X-RAY DIFFRACTIONf_dihedral_angle_d18.3272395
X-RAY DIFFRACTIONf_chiral_restr0.0651007
X-RAY DIFFRACTIONf_plane_restr0.0031101
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.301-3.41890.37364150.31012145100
3.4189-3.5557000.28532531100
3.5557-3.7174000.25432557100
3.7174-3.91320.30583430.24612183100
3.9132-4.158000.22882561100
4.158-4.47850.2273160.19882251100
4.4785-4.9283000.18072575100
4.9283-5.6392000.21652589100
5.6392-7.09630.41452390.31772355100
7.0963-36.62570.18551380.2113252198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.95140.94714.6694.77042.79410.04781.15880.9786-0.5420.4244-0.7087-0.1630.87631.9399-0.5690.95260.1125-0.03111.4374-0.06970.922750.809550.384939.3526
25.91181.15923.47180.16012.32434.0977-0.188-0.70541.51770.2805-0.80090.5572-0.53360.08430.99631.24850.1468-0.12681.3652-0.16731.07348.703961.154546.5497
35.3987-1.45121.490510.5485-0.16194.6087-0.38450.50920.832-0.0623-0.2058-0.1828-0.93340.01690.6020.92140.1828-0.13621.0928-0.01881.084522.167963.983612.8108
45.63813.65453.46647.36520.44469.11540.6099-0.1376-1.11890.658-0.0029-0.2330.5058-0.6972-0.511.01190.18640.02350.9378-0.14580.968317.791141.681320.9137
54.1757-0.65681.95395.3327-1.80989.6248-0.13360.4513-0.0689-0.42940.14170.38211.5495-0.33460.07310.9769-0.07370.08231.5301-0.09910.8326-7.392351.653-20.2417
61.15870.6508-0.10967.46550.91976.1128-0.06090.11-0.3249-0.3948-0.16311.10390.6199-1.64020.25440.6028-0.04760.09151.7666-0.00841.1676-12.326750.13-12.4226
78.8065-0.3643-0.64058.82131.30984.2435-0.16551.07190.613-0.7429-0.08880.2083-0.3271-0.50240.26360.99770.24280.02381.93250.11710.80982.458360.6029-31.1818
83.919-1.95270.294911.7583-1.36095.0124-0.2735-0.5849-0.30180.34720.31041.0568-0.0351-0.8159-0.0290.63940.13960.12751.79950.03760.8274-20.069467.16343.3715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 37:103A37 - 103
2X-RAY DIFFRACTION2chain B and resid 28:103B28 - 103
3X-RAY DIFFRACTION3chain A and resid 104:199A104 - 199
4X-RAY DIFFRACTION4chain B and resid 104:199B104 - 199
5X-RAY DIFFRACTION5chain A and resid 200:269A200 - 269
6X-RAY DIFFRACTION6chain B and resid 200:273B200 - 273
7X-RAY DIFFRACTION7chain A and resid 275:432A275 - 432
8X-RAY DIFFRACTION8chain B and resid 274:434B274 - 434

+
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