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- PDB-7kb3: The structure of a sensor domain of a histidine kinase (VxrA) fro... -

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Basic information

Entry
Database: PDB / ID: 7kb3
TitleThe structure of a sensor domain of a histidine kinase (VxrA) from Vibrio cholerae O1 biovar eltor str. N16961, 2nd form
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


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. ...: / 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 / DI(HYDROXYETHYL)ETHER / S,R MESO-TARTARIC ACID / Sensor histidine kinase VxrA
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionOct 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase
B: Sensor histidine kinase
C: Sensor histidine kinase
D: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,52341
Polymers99,5164
Non-polymers2,00737
Water2,306128
1
A: Sensor histidine kinase
B: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,58219
Polymers49,7582
Non-polymers82417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-90 kcal/mol
Surface area24210 Å2
MethodPISA
2
C: Sensor histidine kinase
D: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,94022
Polymers49,7582
Non-polymers1,18220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-131 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.085, 116.677, 120.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Sensor histidine kinase


Mass: 24878.979 Da / Num. of mol.: 4
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: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KM24

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Non-polymers , 6 types, 165 molecules

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


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


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.04 Å3/Da / Density % sol: 69.52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate:HCl, 1.5 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 16, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→42 Å / Num. obs: 75884 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.028 / Χ2: 0.711 / Net I/σ(I): 25.9
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 3763 / CC1/2: 0.716 / Rpim(I) all: 0.431 / Χ2: 0.453 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R7Q
Resolution: 2.25→41.07 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 3721 4.93 %random
Rwork0.2049 ---
obs0.206 75414 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6866 0 105 128 7099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017150
X-RAY DIFFRACTIONf_angle_d0.4559715
X-RAY DIFFRACTIONf_dihedral_angle_d17.3652579
X-RAY DIFFRACTIONf_chiral_restr0.0361057
X-RAY DIFFRACTIONf_plane_restr0.0041259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.32731160.30172660X-RAY DIFFRACTION100
2.28-2.310.33461260.28652605X-RAY DIFFRACTION100
2.31-2.340.33261460.28212651X-RAY DIFFRACTION100
2.34-2.370.29841160.27592647X-RAY DIFFRACTION100
2.37-2.410.29961430.27092605X-RAY DIFFRACTION100
2.41-2.450.2571290.24972652X-RAY DIFFRACTION100
2.45-2.490.29781320.26412632X-RAY DIFFRACTION99
2.49-2.530.27261580.26772605X-RAY DIFFRACTION100
2.53-2.580.31281470.26432608X-RAY DIFFRACTION99
2.58-2.630.31641450.26752641X-RAY DIFFRACTION100
2.63-2.680.29711130.242591X-RAY DIFFRACTION99
2.68-2.740.26551190.25822679X-RAY DIFFRACTION100
2.74-2.80.2951240.25832681X-RAY DIFFRACTION100
2.8-2.870.26191300.25992632X-RAY DIFFRACTION100
2.87-2.950.31991320.26222672X-RAY DIFFRACTION100
2.95-3.030.29911300.25122636X-RAY DIFFRACTION100
3.03-3.130.31691400.25572655X-RAY DIFFRACTION100
3.13-3.240.30031260.25252653X-RAY DIFFRACTION99
3.24-3.370.27171340.24012657X-RAY DIFFRACTION99
3.37-3.530.27251370.22562637X-RAY DIFFRACTION99
3.53-3.710.23951700.20842643X-RAY DIFFRACTION100
3.71-3.950.18761740.19022639X-RAY DIFFRACTION100
3.95-4.250.18981550.16672655X-RAY DIFFRACTION100
4.25-4.680.17141610.15962692X-RAY DIFFRACTION100
4.68-5.350.18391490.15912663X-RAY DIFFRACTION99
5.35-6.740.20951340.18792761X-RAY DIFFRACTION100
6.74-41.070.1631350.15942841X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.9676-4.05811.27954.144-1.35062.18010.1294-0.84420.30421.19350.3052-1.90480.08251.5151-0.35190.59060.0417-0.11930.7124-0.05380.706931.618524.700334.0908
29.01235.03220.50558.8378-0.95392.90760.257-1.1326-0.28211.3624-0.4103-0.67740.3198-0.00350.04290.83550.0703-0.12410.55870.1320.479616.520410.573443.3652
33.06810.50673.19090.29040.34573.1570.13770.3791-0.016-0.30620.08870.11940.22830.1389-0.11010.59370.01610.03750.48320.08880.5141-1.83429.819425.0646
46.4953-2.1607-3.10699.72630.28055.20310.59960.4793-0.1765-0.7207-0.42831.19630.0933-0.8071-0.13510.5366-0.0385-0.22230.64960.12580.6546-18.31364.970816.3964
52.69020.82221.46114.22581.74513.99740.1559-0.5114-0.19960.6037-0.06840.47450.4359-0.2819-0.06170.5642-0.01640.11990.46460.08810.4909-9.82313.010932.3254
64.38060.8112-4.34414.9969-1.40884.46530.5073-0.00530.91020.3542-0.08580.4378-0.7148-0.5389-0.34850.599-0.0077-0.00360.49760.02080.5196.190415.915835.9582
76.15434.90610.087.73382.29384.88940.0265-0.32390.12390.8219-0.1658-0.27690.05230.21450.19590.51530.1181-0.08460.43290.07060.429318.379421.745938.6692
85.98592.4345-0.94412.42792.45187.2472-0.0215-1.18830.79881.13780.2253-0.32020.4068-0.1841-0.24660.69940.09910.02090.67440.09810.7155.188635.056412.4751
92.09271.1544-1.01936.5355-4.85123.59270.24460.35360.89710.19190.25031.3894-1.0797-1.1868-0.67560.5140.150.05790.5930.17070.735-3.973841.53645.6939
103.9018-0.84381.70027.1677-1.40425.5759-0.04920.86860.0571-0.3360.12780.8534-0.3479-0.6488-0.07460.73730.0530.07170.8186-0.02640.55783.912326.9183-10.5515
112.1848-1.84892.79164.5546-1.49614.69890.3290.2361-0.6074-0.15470.0226-0.53631.10190.1602-0.30581.08210.22670.13740.69-0.12491.102222.56991.17923.505
122.1742-2.22371.61266.865-1.6061.09780.01240.8724-0.5418-1.4527-0.4673-0.06441.15870.2790.42711.45340.35810.1521.0807-0.31781.004121.31892.8462-8.8813
134.2638-2.8014-1.93457.31751.72433.67930.15910.5698-0.0271-0.7092-0.1943-0.3562-0.00810.26670.03330.48340.03660.04690.60360.05110.407410.953729.3573-2.6534
146.7702-0.0031-2.10896.3558-1.70032.3653-0.05871.19441.733-0.88830.0324-0.2068-0.77590.08990.06630.73510.0618-0.03730.66910.1760.713421.417127.172226.7794
157.98530.7791-3.55117.6068-2.90475.8386-0.35830.47820.4357-0.67720.16930.5482-0.0155-0.35290.2580.4683-0.0647-0.13110.54120.05720.4262-9.985523.60614.0428
163.2682.68941.65087.97845.28397.1444-0.1495-0.07430.6121-0.201-0.23471.0651-0.4022-0.66270.45730.40480.0796-0.02430.50670.0030.7135-14.897436.207821.1256
175.60332.03023.22153.05680.23862.2033-0.25440.41-0.1250.10410.2365-0.53620.00790.3055-0.01720.5330.04220.00030.4872-0.05950.55237.463936.874333.41
185.74060.2263-1.89616.29860.24736.6311-0.1815-1.27860.35791.1804-0.0909-0.6944-0.01040.73310.30721.01080.1049-0.40320.8308-0.06820.806719.292841.152548.0102
194.9055-0.1662-0.87366.65011.12863.77350.1675-0.68410.25441.2090.0138-0.00060.133-0.1077-0.19240.6869-0.0026-0.00160.4783-0.07980.35514.432845.476845.0081
203.9592.15692.83046.13332.17892.76310.3842-0.4902-0.20490.817-0.27510.46030.938-0.5668-0.06050.4967-0.0680.04240.418-0.00520.4286-5.867231.469432.3937
214.12434.55732.79148.53335.31175.85110.1160.02170.10280.2971-0.14120.71580.1934-0.24340.01290.36420.0459-0.04710.43810.03810.5328-12.010426.732517.3161
226.7057-0.325.23481.6733-1.71398.5540.21410.2883-1.20540.1913-0.0085-0.50440.23691.2979-0.30110.38550.0237-0.03810.54770.03760.59862.244817.295117.02
236.3145-1.1259-1.52758.16070.9237.83220.1829-0.1313-1.443-0.2439-0.23010.10081.26740.27340.07350.66880.1370.02240.47320.13010.873921.439911.494920.9375
246.51-0.06281.78456.38546.1056.88550.525-0.2723-1.27190.8011-0.41750.13131.08080.1002-0.01880.85030.23910.05030.61110.17960.946626.0296.371829.1317
250.64171.334-0.34883.6206-0.78122.0939-0.0254-0.3263-0.26360.2564-0.0023-0.32630.0270.320.05010.39980.05260.15010.63060.07330.606131.419130.28713.4394
268.38532.9934-2.14945.9513-3.7676.30120.24560.62381.5064-0.132-0.26960.2984-0.8382-0.3002-0.10050.74790.13560.11760.72090.20391.047715.961154.57410.0683
275.6975-2.8378-0.74916.13680.6135.29830.08610.1810.5606-0.0315-0.0048-0.3819-0.58760.163-0.08190.4573-0.04690.14190.41880.03890.521430.624249.48053.7778
280.7741.2957-1.81485.1823-3.97456.8245-0.089-0.1452-0.3605-0.3053-0.2596-0.59830.57350.58560.29550.36570.08420.10250.54670.04840.690132.823424.349211.2117
297.02721.6945-0.65917.7327-1.79727.39830.12850.2264-0.8811-1.1037-0.2012-0.54291.32480.37790.33890.76770.19740.14120.4949-0.02820.727526.90568.143415.6845
309.3329-1.7206-5.31742.46431.75383.4574-0.09250.6489-0.0248-0.240.4408-0.57171.18660.2442-0.41090.55640.0422-0.08380.6267-0.01620.57270.510120.376810.5108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 108 )
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 176 )
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 193 )
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 237 )
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 254 )
9X-RAY DIFFRACTION9chain 'B' and (resid 35 through 50 )
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 68 )
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 122 )
12X-RAY DIFFRACTION12chain 'B' and (resid 123 through 163 )
13X-RAY DIFFRACTION13chain 'B' and (resid 164 through 237 )
14X-RAY DIFFRACTION14chain 'B' and (resid 238 through 254 )
15X-RAY DIFFRACTION15chain 'C' and (resid 38 through 50 )
16X-RAY DIFFRACTION16chain 'C' and (resid 51 through 68 )
17X-RAY DIFFRACTION17chain 'C' and (resid 69 through 87 )
18X-RAY DIFFRACTION18chain 'C' and (resid 88 through 108 )
19X-RAY DIFFRACTION19chain 'C' and (resid 109 through 163 )
20X-RAY DIFFRACTION20chain 'C' and (resid 164 through 193 )
21X-RAY DIFFRACTION21chain 'C' and (resid 194 through 227 )
22X-RAY DIFFRACTION22chain 'C' and (resid 228 through 242 )
23X-RAY DIFFRACTION23chain 'C' and (resid 243 through 254 )
24X-RAY DIFFRACTION24chain 'D' and (resid 35 through 49 )
25X-RAY DIFFRACTION25chain 'D' and (resid 50 through 87 )
26X-RAY DIFFRACTION26chain 'D' and (resid 88 through 108 )
27X-RAY DIFFRACTION27chain 'D' and (resid 109 through 163 )
28X-RAY DIFFRACTION28chain 'D' and (resid 164 through 217 )
29X-RAY DIFFRACTION29chain 'D' and (resid 218 through 237 )
30X-RAY DIFFRACTION30chain 'D' and (resid 238 through 254 )

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