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- PDB-9p6i: Crystal Structure of the Histidine Kinase VC2136 from Vibrio chol... -

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Basic information

Entry
Database: PDB / ID: 9p6i
TitleCrystal Structure of the Histidine Kinase VC2136 from Vibrio cholerae serotype O1
Componentshistidine kinase
KeywordsTRANSFERASE / Center for Structural Biology of Infectious Diseases (CSBID) / Histidine kinase / Structural Genomics
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function
PAS domain / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / PAS domain ...PAS domain / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Wawrzak, Z. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: To Be Published
Title: Crystal Structure of the Histidine Kinase from Vibrio cholerae serotype O1
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Wawrzak, Z. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionJun 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: histidine kinase
B: histidine kinase
C: histidine kinase
D: histidine kinase
E: histidine kinase
F: histidine kinase
G: histidine kinase
H: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,91353
Polymers314,7728
Non-polymers4,14145
Water1,02757
1
A: histidine kinase
B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,94215
Polymers78,6932
Non-polymers1,24913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-185 kcal/mol
Surface area20230 Å2
MethodPISA
2
C: histidine kinase
D: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,49711
Polymers78,6932
Non-polymers8049
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-141 kcal/mol
Surface area19600 Å2
MethodPISA
3
E: histidine kinase
F: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,53212
Polymers78,6932
Non-polymers83910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-146 kcal/mol
Surface area20150 Å2
MethodPISA
4
G: histidine kinase
H: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,94215
Polymers78,6932
Non-polymers1,24913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-185 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.211, 86.211, 212.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
histidine kinase


Mass: 39346.504 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_2136 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: H9L4P6, histidine kinase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 6.5 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3; Screen: Anions (G8), 0.37M Sodium sulfate, 0.1M MES pH 6.5. Cryo: 2M Lithium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97848 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 45970 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 68.8 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.034 / Rsym value: 0.106 / Χ2: 1.136 / Net I/σ(I): 23.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2314 / CC1/2: 0.634 / CC star: 0.881 / Rpim(I) all: 0.418 / Χ2: 0.997 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→28.22 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / SU B: 34.487 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28631 2322 5.1 %RANDOM
Rwork0.24022 ---
obs0.2425 43575 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 93.051 Å2
Baniso -1Baniso -2Baniso -3
1-16.29 Å20 Å20 Å2
2--16.29 Å20 Å2
3----32.58 Å2
Refinement stepCycle: 1 / Resolution: 2.75→28.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10887 0 213 57 11157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01211200
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611037
X-RAY DIFFRACTIONr_angle_refined_deg0.8451.64215186
X-RAY DIFFRACTIONr_angle_other_deg0.6651.5725285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.85351376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.5875120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg2.793101943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0410.21825
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213064
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022488
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3635.6925537
X-RAY DIFFRACTIONr_mcbond_other2.3625.6925537
X-RAY DIFFRACTIONr_mcangle_it3.94410.2226902
X-RAY DIFFRACTIONr_mcangle_other3.94310.2236903
X-RAY DIFFRACTIONr_scbond_it2.3166.1435663
X-RAY DIFFRACTIONr_scbond_other2.2095.9935492
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.74310.958027
X-RAY DIFFRACTIONr_long_range_B_refined8.18760.712920
X-RAY DIFFRACTIONr_long_range_B_other8.14860.6812914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 156 -
Rwork0.305 3241 -
obs--99.71 %
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)
12.5426-0.1924-0.6642.7542-1.70821.3653-0.0261-0.17351.7754-0.2790.2441-0.4080.13770.2887-0.21790.6448-0.24040.11821.4743-0.47081.390741.9930.21442.367
22.74240.6914-0.8136.69481.97086.12370.3441-0.34270.54510.09650.171-0.25290.15570.1374-0.51510.22870.0331-0.10550.1103-0.12410.338624.24929.60651.335
38.18774.1216-0.00024.22230.26590.3530.1341-0.57830.39640.1063-0.10150.05830.26820.1043-0.03260.29220.0699-0.05580.1522-0.05610.060317.04912.68847.488
415.56388.25221.4034.38720.58543.3486-0.7351-1.0287-0.8837-0.3437-0.5186-0.524-0.0062-0.45371.25370.66240.1440.19510.6829-0.04490.6287-30.0254.02656.503
517.4404-0.5767-5.24120.46710.49121.85120.0599-0.098-0.13890.0453-0.16640.081-0.111-0.0860.10640.3345-0.0079-0.03760.0974-0.06320.0784-10.1719.33554.278
64.529-2.5173.74731.4526-2.14033.17780.85711.7815-0.0979-0.2565-0.9558-0.07150.49411.57540.09861.15580.25210.10961.6035-0.64931.869547.822439.512
74.7684-1.31061.8672.27290.91597.10150.07770.0209-0.00730.16660.287-0.46070.3683-0.157-0.36480.2970.17110.02840.1989-0.09270.255338.29711.32630.303
812.1231-0.2953-3.33010.0866-0.17721.7890.23740.27490.2468-0.0489-0.02340.04360.0617-0.0683-0.2140.30890.0561-0.10380.0642-0.03210.0654.3516.26839.437
912.9673-7.6717-0.99874.7820.03471.4169-0.238-0.0469-1.02030.02-0.07560.5610.23220.18930.31360.18420.0294-0.00510.2283-0.22770.4898-31.46415.20750.141
1016.4179-5.3323-1.30197.89130.17630.1283-0.407-0.30890.29440.73370.43680.54540.0229-0.0381-0.02980.26730.02590.00090.2724-0.03610.1257-15.2530.92742.741
117.91570.1275-3.341.89730.10641.42480.4517-0.0640.81190.2726-0.0454-0.6998-0.19680.0161-0.40630.47120.03250.00260.1871-0.06090.39113.71356.23765.841
123.8914-0.1901-0.23214.21511.56223.1160.1647-0.00280.07130.0761-0.2972-0.259-0.1385-0.30440.13250.16980.0510.00180.08940.00420.15911.01643.65158.228
131.2144-0.99310.37057.10691.92331.59240.0935-0.3264-0.02910.88570.1413-0.190.7030.0712-0.23480.71040.0348-0.11380.18690.00610.09724.4362.14257.31
142.19982.0037-0.89272.1938-1.19680.7662-0.4679-0.5265-1.3937-0.02410.1877-0.979-0.2899-0.46490.28011.3520.63150.41481.40370.891.179719.606-19.06945.005
152.5805-4.2924-0.94516.36329.28847.10050.0258-0.155-0.2420.63660.3228-0.06710.62570.3805-0.34870.3080.034-0.08020.2649-0.0140.071110.812-1.0753.569
162.63870.80680.9013.27760.72342.58490.25340.35970.18810.2332-0.36960.75360.2965-0.17720.11620.45490.00180.12710.3256-0.10180.2678-10.17148.07472.143
175.344-6.7342-1.955211.35894.60022.7082-0.3584-0.79350.28360.97120.551-0.27080.59070.2129-0.19260.50540.04160.00630.3736-0.09860.11571.58610.36865.862
189.083-0.47641.50121.5742.59314.86040.65890.87240.3357-0.1996-0.2615-0.2844-0.19-0.2612-0.39740.13610.08940.03640.2150.13630.188628.579-19.34353.86
190.3598-0.73570.55261.5958-1.48262.2092-0.4128-0.3218-0.23690.66110.42520.3970.0480.4138-0.01241.17250.70220.33091.21590.13620.726314.02-16.96762.529
2033.45480.03130.905528.72962.76260.2906-0.4569-0.4244-1.64070.47560.5271-0.29090.02180.0462-0.07020.4049-0.04770.01670.13110.05020.0949-0.096-7.25864.5
210.1637-0.6156-2.7592.491311.407152.5559-0.04730.20490.00430.0531-0.52890.08580.1345-2.0060.57620.3569-0.10340.09280.69130.1080.4635-56.353-36.48533.652
220.4362-0.2071-1.7174.4161-2.1749.0347-0.26470.3682-0.0450.21470.11240.27210.6008-1.83010.15230.6215-0.0531-0.21110.690.02160.5838-46.211-21.6728.412
236.0143-0.54163.13865.2242-2.428512.8727-0.4261-0.24740.091-0.2810.22330.56370.1578-0.25120.20280.14840.073-0.09710.07-0.04240.3011-44.303-9.121.545
246.70734.666-0.38045.2282.19713.397-0.101-0.03330.1051-0.2867-0.02620.1796-0.2568-0.08130.12720.31980.0561-0.17870.12450.00630.1529-33.967-11.83619.574
250.98610.84020.09363.4096-1.32071.22820.07440.2802-0.05240.0234-0.2722-0.4444-0.18310.14540.19790.33960.0201-0.08150.24680.07240.1354-0.71112.02918.902
264.5878-2.2198-1.87361.41850.51511.2322-0.12150.58540.1748-0.18690.29540.09220.2724-0.9309-0.17390.5731-0.2336-0.25251.12860.18480.5612-44.379-29.61531.531
270.98840.76673.05364.87282.83269.84970.05510.053-0.0892-0.1415-0.0298-0.02130.13670.1868-0.02540.12960.0809-0.04080.1180.01890.2048-28.586-31.8940.293
2815.5331-2.0602-4.04415.06510.58531.63930.3680.4216-0.3605-0.1765-0.2304-0.3504-0.3544-0.2907-0.13770.39170.06820.01380.19480.0790.1576-27.7-23.18741.903
2916.423710.9963-1.54078.3914-1.92880.9360.0598-0.1950.05140.0716-0.01810.0624-0.015-0.0428-0.04170.20680.0877-0.03270.1522-0.05540.03-17.877-14.06535.43
300.71042.0116-0.36199.102-2.23420.6193-0.1685-0.10940.13140.0210.22280.2945-0.0992-0.1169-0.05430.2792-0.0056-0.11060.2331-0.00880.11942.4623.5524.527
312.9902-1.8301-2.39064.9328-2.05465.16080.34630.4745-0.0105-0.539-0.14290.20010.032-0.5404-0.20340.29790.0720.00250.42760.10120.3908-50.12626.0793.588
325.93970.1308-0.5747.06831.91653.57040.00150.05230.10390.01780.2650.1577-0.1591-0.1241-0.26650.14190.10780.0130.09280.02420.1151-44.44112.48813.097
330.8142-1.30491.32494.2386-0.12794.05250.0520.3336-0.07260.1328-0.01510.25030.28530.9137-0.03690.24340.21730.05840.65090.0760.1084-10.7574.36111.191
344.4867-8.07214.629528.1735-10.40185.4083-0.3796-0.37120.33961.66170.1514-0.5377-0.6137-0.57950.22820.4750.3381-0.23320.5072-0.1220.220111.416-25.16121.865
359.4494-9.95528.092112.063-9.13949.25970.57180.0728-0.3047-1.40990.1530.17461.42260.1485-0.72480.75480.1443-0.13810.3744-0.13540.1627-1.446-15.39619.674
362.43534.0411-0.79256.7735-1.40640.43330.30520.01130.49780.35150.04750.89380.0688-0.2816-0.35270.61320.14110.07361.02660.250.6642-46.75732.413.501
379.3566-4.1621-1.27646.70980.75952.6133-0.08410.57970.67440.33320.1226-0.2040.0407-0.2783-0.03860.13740.0055-0.01630.15830.10310.1118-29.74334.649-2.453
385.3488-6.48282.00598.0377-1.86542.5915-0.0926-0.212-0.10890.21150.35880.08660.25750.1598-0.26610.14920.0810.05780.23770.07080.1401-18.82712.2611.349
396.8129-3.5958-1.83671.9050.95710.56320.01660.5606-0.4110.0584-0.29540.1879-0.1527-0.19290.27870.65470.063-0.3620.2344-0.16930.4433-0.502-28.73914.417
401.1210.48851.5980.22520.72452.3477-0.1827-0.10450.0622-0.0722-0.0240.0743-0.1962-0.08470.20670.45310.09110.14040.329-0.00670.25665.582-17.2438.045
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 50
2X-RAY DIFFRACTION2A51 - 86
3X-RAY DIFFRACTION3A87 - 136
4X-RAY DIFFRACTION4A137 - 164
5X-RAY DIFFRACTION5A165 - 192
6X-RAY DIFFRACTION6B12 - 43
7X-RAY DIFFRACTION7B44 - 107
8X-RAY DIFFRACTION8B108 - 141
9X-RAY DIFFRACTION9B142 - 171
10X-RAY DIFFRACTION10B172 - 187
11X-RAY DIFFRACTION11C15 - 43
12X-RAY DIFFRACTION12C44 - 106
13X-RAY DIFFRACTION13C107 - 159
14X-RAY DIFFRACTION14C160 - 169
15X-RAY DIFFRACTION15C170 - 187
16X-RAY DIFFRACTION16D15 - 105
17X-RAY DIFFRACTION17D106 - 145
18X-RAY DIFFRACTION18D146 - 163
19X-RAY DIFFRACTION19D164 - 177
20X-RAY DIFFRACTION20D178 - 186
21X-RAY DIFFRACTION21E12 - 16
22X-RAY DIFFRACTION22E17 - 42
23X-RAY DIFFRACTION23E43 - 70
24X-RAY DIFFRACTION24E71 - 105
25X-RAY DIFFRACTION25E106 - 192
26X-RAY DIFFRACTION26F12 - 43
27X-RAY DIFFRACTION27F44 - 75
28X-RAY DIFFRACTION28F76 - 99
29X-RAY DIFFRACTION29F100 - 126
30X-RAY DIFFRACTION30F127 - 187
31X-RAY DIFFRACTION31G15 - 39
32X-RAY DIFFRACTION32G40 - 103
33X-RAY DIFFRACTION33G104 - 143
34X-RAY DIFFRACTION34G144 - 160
35X-RAY DIFFRACTION35G161 - 188
36X-RAY DIFFRACTION36H15 - 43
37X-RAY DIFFRACTION37H44 - 90
38X-RAY DIFFRACTION38H91 - 141
39X-RAY DIFFRACTION39H142 - 159
40X-RAY DIFFRACTION40H160 - 186

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