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- PDB-7la6: THE STRUCTURE OF A SENSOR DOMAIN OF A HISTIDINE KINASE (VxrA) FRO... -

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Basic information

Entry
Database: PDB / ID: 7la6
TitleTHE STRUCTURE OF A SENSOR DOMAIN OF A HISTIDINE KINASE (VxrA) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961, N239 deletion mutant
ComponentsSensor histidine kinase
KeywordsSIGNALING PROTEIN / VXRA / TWO-COMPONENT SYSTEM / HISTIDINE KINASE / SENSOR DOMAIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / 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. ...: / 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 superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Sensor histidine kinase VxrA
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsTan, K. / Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
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
DepositionJan 5, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJan 27, 2021ID: 7KB4
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)25,85611
Polymers24,7651
Non-polymers1,09110
Water1,22568
1
A: Sensor histidine kinase
hetero molecules

A: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,71222
Polymers49,5302
Non-polymers2,18220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7380 Å2
ΔGint-99 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.654, 87.654, 106.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sensor histidine kinase


Mass: 24764.877 Da / Num. of mol.: 1 / Mutation: N239 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0565 / Plasmid: PMCSG57 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -MAGI / References: UniProt: Q9KM24

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Non-polymers , 5 types, 78 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M LITHIUM SULFIDE, 0.1 M SODIUM, CACODYLATE:HCL, 30% (W/V) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 5, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→46 Å / Num. obs: 29036 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 40.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.027 / Rrim(I) all: 0.076 / Χ2: 1.574 / Net I/σ(I): 42.2
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1416 / CC1/2: 0.747 / Rpim(I) all: 0.302 / Rrim(I) all: 0.845 / Χ2: 0.741 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.18.2_3874refinement
HKL-3000data scaling
HKL-3000data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R7Q

4r7q


Resolution: 1.98→45.42 Å / SU ML: 0.1838 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1469 5.07 %random
Rwork0.1813 27509 --
obs0.1827 28978 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.98 Å2
Refinement stepCycle: LAST / Resolution: 1.98→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 68 68 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01691889
X-RAY DIFFRACTIONf_angle_d1.52372554
X-RAY DIFFRACTIONf_chiral_restr0.0843269
X-RAY DIFFRACTIONf_plane_restr0.0097325
X-RAY DIFFRACTIONf_dihedral_angle_d23.7266701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.050.29571320.2332374X-RAY DIFFRACTION87.56
2.05-2.140.23111380.21322751X-RAY DIFFRACTION99.97
2.14-2.230.24161540.22735X-RAY DIFFRACTION100
2.23-2.350.2411450.20462729X-RAY DIFFRACTION99.97
2.35-2.50.24221610.19382747X-RAY DIFFRACTION100
2.5-2.690.23461470.20522767X-RAY DIFFRACTION99.97
2.69-2.960.2411580.20682763X-RAY DIFFRACTION100
2.96-3.390.25481330.19882810X-RAY DIFFRACTION99.9
3.39-4.270.17521460.16142841X-RAY DIFFRACTION99.9
4.27-45.420.17971550.16182992X-RAY DIFFRACTION99.81
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)
13.42382293498-4.21077895425-0.9386267051288.470909908933.760551745584.96362695693-0.10458505983-0.0750291542846-0.1749735887671.011608072980.160228791326-0.007773261779540.624369361248-0.0132393363847-0.05285452847880.43948250986-0.02660400993620.005153445757180.2821828448090.102901948470.33721871314815.893137685714.401039233519.7060052246
24.17070790928-0.3799574398411.68350560983.64034222280.2374841108624.82734501715-0.1055229463930.009150417805170.321478726313-0.1357367065970.05283014894950.184336812286-0.498666594594-0.470652954840.02120079617550.2867292259420.03170570327130.002473571829310.224705270630.0176141123480.2511683441160.99063266116946.559072890511.3502263061
32.02001706006-3.84318865064-0.5532979471328.449268510071.493670286090.761881706680.000971807613637-0.00853019116846-0.04087967977130.004705694820430.0238526031577-0.1554697944190.1352582936290.0924797632742-0.02642306832010.3670059615890.00595893939322-0.02277884965770.2438868832660.01354744355010.32785799353617.306979598220.806786505415.0715438706
43.872359010640.4763414629052.906457997821.99042613475-1.140602173147.79425857999-0.317409294838-0.1830576302750.3243352538130.5984017246750.2324994693930.434050591352-0.443409301943-0.7307311475960.06380972427230.3634234755850.07619619310440.01534722109450.3525192925220.06477314306440.43525128581510.96720740114.9713987701-2.2767850649
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 36 through 68 )36 - 681 - 34
22chain 'A' and (resid 69 through 176 )69 - 17635 - 145
33chain 'A' and (resid 177 through 228 )177 - 228146 - 198
44chain 'A' and (resid 229 through 254 )229 - 254199 - 225

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