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- PDB-4r7q: The structure of a sensor domain of a histidine kinase from Vibri... -

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Basic information

Entry
Database: PDB / ID: 4r7q
TitleThe structure of a sensor domain of a histidine kinase from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsSensor histidine kinase
KeywordsSIGNALING PROTEIN / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / plasma membrane
Similarity search - Function
: / Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...: / Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ACETATE ION / Sensor histidine kinase VxrA
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.981 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Bacteriol. / Year: 2021
Title: Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae - A Hairpin-swapped Dimer and its Conformational Change.
Authors: Tan, K. / Teschler, J.K. / Wu, R. / Jedrzejczak, R.P. / Zhou, M. / Shuvalova, L.A. / Endres, M.J. / Welk, L.F. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Yildiz, F.H. / Joachimiak, A.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6027
Polymers25,0671
Non-polymers5356
Water1,60389
1
A: Sensor histidine kinase
hetero molecules

A: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,20414
Polymers50,1332
Non-polymers1,07112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5520 Å2
ΔGint-131 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.600, 88.600, 106.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Sensor histidine kinase


Mass: 25066.559 Da / Num. of mol.: 1 / Fragment: sensor domain (UNP residues 38-256)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: N16961 / Gene: VC_A0565, Vibrio cholerae / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q9KM24
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8M Lithium sulfate monohydrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2014 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.98→37.2 Å / Num. all: 30252 / Num. obs: 30252 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 11.5 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 49.8
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 4 / Num. unique all: 1488 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.981→37.157 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 1530 5.07 %random
Rwork0.1838 ---
obs0.1847 30175 99.72 %-
all-30175 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.981→37.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 30 89 1761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061741
X-RAY DIFFRACTIONf_angle_d12374
X-RAY DIFFRACTIONf_dihedral_angle_d11.975610
X-RAY DIFFRACTIONf_chiral_restr0.068260
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.981-2.0450.22651360.22312523X-RAY DIFFRACTION99
2.045-2.11810.25881440.21822554X-RAY DIFFRACTION100
2.1181-2.20290.19031420.19912573X-RAY DIFFRACTION100
2.2029-2.30310.22821340.19092554X-RAY DIFFRACTION100
2.3031-2.42450.21931200.19052599X-RAY DIFFRACTION100
2.4245-2.57640.25181410.22582X-RAY DIFFRACTION100
2.5764-2.77520.23041380.21942605X-RAY DIFFRACTION100
2.7752-3.05440.21081540.21192595X-RAY DIFFRACTION100
3.0544-3.49610.20141370.19272620X-RAY DIFFRACTION100
3.4961-4.40360.17531460.15232658X-RAY DIFFRACTION100
4.4036-37.16350.19411380.17322782X-RAY DIFFRACTION98
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)
13.0721-4.5895-3.52439.34072.07248.5657-0.1397-0.0678-1.27190.89780.06071.72031.3589-0.77820.09460.6184-0.02820.03020.38710.05670.687316.97565.049515.197
26.444-5.5322-1.13067.00722.79963.024-0.5905-0.92610.0571.01360.6836-0.63150.49170.5145-0.03820.84090.10030.0280.41860.08860.426616.483824.381225.2842
33.286-2.59233.30473.3929-3.41598.91280.12460.0456-0.20740.069-0.0670.27340.6224-0.6472-0.08390.3713-0.04010.00480.3189-0.04270.29622.036137.54849.0591
44.29814.80783.98346.26185.71877.8305-0.42330.94510.9786-1.03760.39411.4881-1.6713-0.4665-0.01010.67250.1109-0.00370.44410.03130.431-4.710151.06030.1373
53.91293.5338-1.03883.4597-2.01866.5183-0.86650.48180.5759-0.4250.73980.9266-1.5262-1.01070.14860.72110.1529-0.08690.55010.01630.5053-6.999653.40869.5746
63.86980.6981.57912.7375-0.08644.62620.0219-0.17140.35550.0171-0.09060.1124-0.6927-0.27790.02960.41080.02580.00760.2191-0.03410.26865.29448.504316.0649
72.8991-3.3204-0.55974.1747-0.31783.5327-0.10120.3157-0.309-0.076-0.00440.04140.13070.13910.08110.41540.0231-0.05450.2790.00680.364815.535928.736114.2088
87.9-7.6356-2.64388.61793.97034.7894-0.3751-0.31870.15080.88380.36420.03180.36440.13080.06130.5450.00470.00310.24340.05050.408220.70117.191618.1095
94.0145.1735.39787.22945.9818.6091-1.33480.31740.91710.18270.26331.7292-1.2984-1.47751.160.77630.161-0.04510.75160.080.695413.634314.37272.9635
105.6156-4.9793-5.72374.51894.65266.9113-0.3915-0.7455-1.97050.4349-0.23680.8780.4737-0.14730.63430.47570.0670.02710.62080.12930.811411.836614.0256-8.331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 100 )
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 170 )
7X-RAY DIFFRACTION7chain 'A' and (resid 171 through 203 )
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 228 )
9X-RAY DIFFRACTION9chain 'A' and (resid 229 through 242 )
10X-RAY DIFFRACTION10chain 'A' and (resid 243 through 253 )

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