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- PDB-4i5s: Structure and function of sensor histidine kinase -

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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 / regulation of DNA-templated transcription / membrane
Similarity search - Function
Histidine kinase, HAMP domain / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...Histidine kinase, HAMP domain / 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-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 / 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 / Histidine kinase-like ATPases / PAS domain superfamily / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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