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- PDB-6nb0: Crystal structure of Histidine kinase from Burkholderia phymatum ... -

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Basic information

Entry
Database: PDB / ID: 6nb0
TitleCrystal structure of Histidine kinase from Burkholderia phymatum STM815
ComponentsHistidine kinase
KeywordsTRANSFERASE / SSGCID / Burkholderia phymatum / Histidine kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyHis 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 / phosphorelay sensor kinase activity / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase/HSP90-like ATPase superfamily / Histidine kinase
Function and homology information
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Histidine kinase from Burkholderia phymatum STM815
Authors: Abendroth, J. / Conrady, D.C. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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

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Assembly

Deposited unit
A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0182
Polymers30,9261
Non-polymers921
Water3,621201
1
A: Histidine kinase
hetero molecules

A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0364
Polymers61,8522
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2750 Å2
ΔGint-18 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.600, 77.600, 97.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histidine kinase / / BuphA.01664.a.A1


Mass: 30925.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_4385
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B2JQF9
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.73 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Rigaku Reagents Wizard 3/4 screen, condition C2: 24% PEG 1500, 20% glycerol + BuphA.01664.a.A1.PW32082 at 33.15mg/ml. Cryo: direct, tray: 224038 D2, puck mtz8-10. Phasing: Molecular ...Details: Rigaku Reagents Wizard 3/4 screen, condition C2: 24% PEG 1500, 20% glycerol + BuphA.01664.a.A1.PW32082 at 33.15mg/ml. Cryo: direct, tray: 224038 D2, puck mtz8-10. Phasing: Molecular dimensions PACT screen condition d3: 24% PEG 1500, 100mM MMT buffer pH 6.0 + BuphA.01664.a.A1.PW32082 at 33.15mg/ml. The crystal was soaked for 20sec solution reservoir + 20% 2.5M Sodium iodide in ethylene glycol, and vitrified in liquid nitrogen. Tray 223760 d3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→39.373 Å / Num. obs: 27087 / % possible obs: 99.4 % / Redundancy: 11.488 % / Biso Wilson estimate: 40.456 Å2 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.031 / Χ2: 0.957 / Net I/σ(I): 46.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
1.9-1.954.8480.2995.4519460.33598
1.95-26.510.3126.1519310.33999.6
2-2.067.9750.2229.618620.23899.9
2.06-2.128.8770.1812.4118160.19299.9
2.12-2.199.8970.16414.8617710.17399.6
2.19-2.2710.6870.11423.617420.1299.6
2.27-2.3611.5460.11223.3216290.11898.6
2.36-2.4512.8060.08929.8515830.09399.9
2.45-2.5614.4060.0713915270.07499.5
2.56-2.6914.3870.0644.5614920.06299.7
2.69-2.8314.4840.04554.6413900.04799.4
2.83-314.4870.03960.4713160.04199.5
3-3.2114.4720.03269.2512760.03499.6
3.21-3.4714.5520.02784.2611500.02899.7
3.47-3.814.3380.02699.3510780.02799.3
3.8-4.2514.3190.02113.219860.02199.3
4.25-4.9114.1230.017135.578750.01899.8
4.91-6.0114.090.018126.467590.01999.7
6.01-8.513.6080.017131.716020.017100
8.5-39.37312.0840.014150.563560.01597.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_3304refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→39.373 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.44
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1345 4.97 %0
Rwork0.1913 ---
obs0.1928 27051 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.38 Å2 / Biso mean: 45.2647 Å2 / Biso min: 19.43 Å2
Refinement stepCycle: final / Resolution: 1.9→39.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 6 206 1795
Biso mean--56.08 49.23 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081688
X-RAY DIFFRACTIONf_angle_d0.8792317
X-RAY DIFFRACTIONf_dihedral_angle_d13.6881046
X-RAY DIFFRACTIONf_chiral_restr0.056281
X-RAY DIFFRACTIONf_plane_restr0.005306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.96790.24481270.21352489261698
1.9679-2.04670.25231150.202925782693100
2.0467-2.13990.23281280.203725412669100
2.1399-2.25270.22281520.204925142666100
2.2527-2.39380.22791350.19792546268199
2.3938-2.57860.20011380.192325642702100
2.5786-2.8380.21131440.180525362680100
2.838-3.24850.20621340.180325982732100
3.2485-4.09210.21891290.1792614274399
4.0921-39.38160.23311430.200227262869100
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)
12.67562.5416-0.31272.6681-0.53472.1907-0.1610.10070.44460.27090.31990.6977-0.0694-0.5315-0.11180.29440.04250.08480.32360.13110.442114.91094.76914.5373
24.82141.44332.46261.510.24411.64210.10920.2752-0.1459-0.0019-0.2585-0.0683-0.3125-0.0618-0.02261.37580.46580.28690.95310.05720.717610.68754.020425.2635
31.74550.60650.1253.15610.78273.2324-0.0534-0.00750.02490.0810.1431-0.01-0.1205-0.1326-0.08720.17770.03290.00790.1840.0190.186128.679914.95359.6678
47.71450.982-0.04237.79990.7487.86490.19920.11370.44780.21470.3210.4259-0.7361-0.8166-0.30720.28430.10210.06250.20870.05530.318522.02821.867211.3002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 58 )A21 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 106 )A59 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 239 )A107 - 239
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 265 )A240 - 265

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