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Basic information

Entry
Database: PDB / ID: 5bwj
TitleStructural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor
ComponentsSensory transduction histidine kinase, putative
KeywordsSIGNALING PROTEIN / periplasmic sensor domain / Lyme disease / Venus Fly Trap fold
Function / homology
Function and homology information


phosphorelay sensor kinase activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
HPT domain superfamily / 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 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain ...HPT domain superfamily / 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 / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Periplasmic binding protein-like II / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Sensory transduction histidine kinase, putative
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsBauer, W.J. / Luthra, A. / Zhu, G. / Radolf, J.D. / Malkowski, M.G. / Caimano, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI 29735 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 094611 United States
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor: A system for sensing small molecules associated with tick feeding.
Authors: Bauer, W.J. / Luthra, A. / Zhu, G. / Radolf, J.D. / Malkowski, M.G. / Caimano, M.J.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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: Sensory transduction histidine kinase, putative
B: Sensory transduction histidine kinase, putative
C: Sensory transduction histidine kinase, putative
D: Sensory transduction histidine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,02213
Polymers106,5014
Non-polymers5209
Water4,630257
1
A: Sensory transduction histidine kinase, putative
B: Sensory transduction histidine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5237
Polymers53,2512
Non-polymers2725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-12 kcal/mol
Surface area16970 Å2
MethodPISA
2
C: Sensory transduction histidine kinase, putative
D: Sensory transduction histidine kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4996
Polymers53,2512
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-21 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.300, 62.853, 111.808
Angle α, β, γ (deg.)90.000, 101.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sensory transduction histidine kinase, putative


Mass: 26625.326 Da / Num. of mol.: 4 / Fragment: residues 23-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0420 / Plasmid: pET28a / Details (production host): NheI/XhoI-digested / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: O51381
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.02 Å3/Da / Density % sol: 34.78 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: D1 samples were concentrated to 1.7 mg/ml in 50 mM Tris (pH 7.5), 50 mM NaCl and 1 mM Tris (2-carboxyethyl) phosphine (TCEP). Crystals grown in 0.1M Tris-HCl (pH 8.0), 0.1 M Mg(NO3)2 and 18% ...Details: D1 samples were concentrated to 1.7 mg/ml in 50 mM Tris (pH 7.5), 50 mM NaCl and 1 mM Tris (2-carboxyethyl) phosphine (TCEP). Crystals grown in 0.1M Tris-HCl (pH 8.0), 0.1 M Mg(NO3)2 and 18% PEG 20,000 equilibrated by hanging drop

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.05→37.66 Å / Num. obs: 49534 / % possible obs: 99.55 % / Redundancy: 3.3 % / Rsym value: 0.063 / Net I/σ(I): 8.82
Reflection shellResolution: 2.0538→2.1052 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.79 / % possible all: 99.03

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.054→37.66 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 1996 4.03 %
Rwork0.1934 47528 -
obs0.1945 49524 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 254.67 Å2 / Biso mean: 54.7777 Å2 / Biso min: 22.98 Å2
Refinement stepCycle: final / Resolution: 2.054→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 33 257 6628
Biso mean--98.42 45.92 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036507
X-RAY DIFFRACTIONf_angle_d0.6418814
X-RAY DIFFRACTIONf_chiral_restr0.0281005
X-RAY DIFFRACTIONf_plane_restr0.0021128
X-RAY DIFFRACTIONf_dihedral_angle_d10.1362278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0538-2.10520.32791490.29573246339595
2.1052-2.16210.29871320.272533843516100
2.1621-2.22570.30741390.26233563495100
2.2257-2.29760.29231300.246733923522100
2.2976-2.37970.25381610.240133743535100
2.3797-2.47490.25271290.232233923521100
2.4749-2.58750.25091370.219433953532100
2.5875-2.72390.28881500.217534033553100
2.7239-2.89450.2691440.216133993543100
2.8945-3.11790.22561410.211233993540100
3.1179-3.43150.22331460.194734153561100
3.4315-3.92760.19941430.172534333576100
3.9276-4.94660.16251430.141934373580100
4.9466-37.67010.19921520.180435033655100
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)
11.41890.26161.50992.45390.07681.63350.04370.3383-0.3096-0.13130.0533-0.07180.07320.3450.01660.30610.06150.02530.398-0.06890.2748-21.1295-27.0959-34.8493
20.5684-1.25690.54472.7807-1.20410.5213-0.354-0.33060.01470.66820.1303-0.0876-0.2526-0.3028-0.35040.3860.01980.0790.3983-0.03750.2189-22.9725-23.3609-21.2182
32.7385-0.57440.26931.8716-0.58971.0579-0.2525-0.32540.35350.26820.08630.0777-0.0382-0.1549-0.00280.30080.02990.01950.3451-0.04850.3207-37.4971-15.1299-25.9391
42.2328-0.35150.90221.2304-0.23211.1874-0.0740.03980.24310.0424-0.08360.1358-0.0562-0.065600.2618-0.0050.03430.28550.00760.2802-38.6151-17.0343-32.7286
50.121-0.44670.19442.8856-2.4072.6112-0.16250.40420.28090.1205-0.2045-0.4226-0.66690.9947-0.06630.2759-0.06280.03910.53860.13520.3006-12.4639-15.7864-33.6656
60.8573-1.3765-0.14112.6059-0.41841.0712-0.01740.37910.0688-0.2594-0.1985-0.03210.1032-0.021100.3523-0.0206-0.04130.39820.03420.2989-42.8316-2.5179-51.1163
70.01390.15430.06211.71110.67950.2733-0.05810.44060.3561-0.1567-0.1075-0.79750.34850.43460.08170.3588-0.00920.06320.5950.14360.3412-28.8621-3.7402-54.594
80.9688-0.0109-0.54222.1564-0.16820.3170.15820.7126-0.1028-0.3329-0.12470.06670.28020.30060.04880.46430.12710.04610.6174-0.02610.2266-29.1035-20.6471-59.4907
91.3868-1.61760.75672.149-1.27631.04040.12230.38990.06660.0279-0.1726-0.05990.13070.19770.00320.3667-0.00140.05570.5676-0.00610.3174-31.8657-14.0801-51.9427
100.0053-0.00370.01310.0024-0.00890.037-0.3772-0.56630.61580.545-0.4363-0.8874-0.36830.15590.00250.59330.0321-0.1240.58690.05240.5793-33.8497-0.3802-36.6424
111.11530.03950.28671.5507-0.65861.07370.27610.0983-0.1218-0.0484-0.0473-0.01620.03250.535900.33270.0415-0.00280.2988-0.06260.3332-18.299223.8128-25.4322
120.7962-0.50920.34131.9475-0.94992.58970.34240.1208-0.20610.18690.4440.7697-0.2007-0.73941.27780.31150.06460.00190.37240.07760.4865-29.641322.7311-25.5133
130.05430.3315-0.03783.0643-1.61361.83-0.0755-0.05390.11480.09630.25250.69760.3725-0.33580.08920.42150.01540.13770.43380.02490.5072-27.591110.7269-11.3825
141.04-0.9607-0.05871.2601-0.77691.8604-0.1017-0.36870.00870.62170.08160.7859-0.2056-0.4718-0.1990.4570.07910.22190.3958-0.01660.5833-26.564416.8572-4.5879
150.36030.19030.61930.55411.49774.09160.0964-0.1233-0.3272-0.06020.1270.63880.9031-0.3418-0.55040.2421-0.06990.01540.32230.08290.6277-27.31449.1938-17.608
160.1354-0.0279-0.06420.3229-0.14850.11330.03430.7746-0.3028-0.8627-0.04940.44760.0020.1363-0.01640.53850.0844-0.11160.3472-0.08930.5474-18.571213.5566-34.3309
171.2826-0.00350.1231.9467-0.46462.45060.1012-0.248-0.04840.8176-0.1379-0.3941-0.12610.154-0.00080.4905-0.0363-0.06810.29170.00550.3464-5.6541-1.6865-4.2206
180.85970.13110.23581.68930.28471.47020.04450.21540.0211-0.0635-0.1078-0.2536-0.16690.2116-0.00010.30050.0186-0.00130.34980.01270.40741.04958.9781-19.6971
190.535-0.32560.31822.4401-0.21421.94840.02880.10240.29480.2348-0.0723-0.3527-0.30150.09300.3842-0.0512-0.04360.38920.03150.46660.288219.4765-14.6184
200.96381.07050.73251.22070.72190.82140.19320.0042-0.13060.0977-0.2323-0.03330.12920.0038-0.12280.2880.0187-0.01540.2748-0.03320.3583-10.4184-6.0856-15.261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 74 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 89 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 170 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 218 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 234 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 86 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 111 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 112 through 170 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 171 through 227 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 228 through 237 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 26 through 64 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 65 through 96 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 97 through 135 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 136 through 198 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 199 through 218 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 219 through 237 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 27 through 86 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 87 through 150 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 151 through 205 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 206 through 237 )D0

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