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- PDB-3mr0: Crystal Structure of Sensory Box Histidine Kinase/Response Regula... -

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Basic information

Entry
Database: PDB / ID: 3mr0
TitleCrystal Structure of Sensory Box Histidine Kinase/Response Regulator from Burkholderia thailandensis E264
ComponentsSensory box histidine kinase/response regulator
Keywordstranscription regulator / PAS fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphorelay sensor kinase activity / membrane => GO:0016020 / protein dimerization activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #490 / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / PAS fold-3 / PAS fold / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #490 / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / PAS fold-3 / PAS fold / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Histidine kinase domain / Histidine kinase domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Response regulator receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Beta-Lactamase / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Helix non-globular / Histidine kinase/HSP90-like ATPase superfamily / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Sensory box histidine kinase/response regulator
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.493 Å
AuthorsKim, Y. / Tesar, C. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Sensory Box Histidine Kinase/Response Regulator from Burkholderia thailandensis E264
Authors: Kim, Y. / Tesar, C. / Buck, K. / Joachimiak, A.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensory box histidine kinase/response regulator
B: Sensory box histidine kinase/response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,44818
Polymers33,4542
Non-polymers1,99416
Water6,449358
1
A: Sensory box histidine kinase/response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7249
Polymers16,7271
Non-polymers9978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensory box histidine kinase/response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7249
Polymers16,7271
Non-polymers9978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.265, 35.080, 71.348
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sensory box histidine kinase/response regulator


Mass: 16727.035 Da / Num. of mol.: 2 / Fragment: residues 106-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_II1009 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q2T6J3

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Non-polymers , 6 types, 374 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M TRIS pH 8.5, 40 %v/v PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 4, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.493→30.578 Å / Num. all: 46689 / Num. obs: 46689 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18.63 Å2 / Rsym value: 0.064 / Net I/σ(I): 17.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1820 / Rsym value: 0.373 / % possible all: 75.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.493→30.578 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2387 5.11 %random
Rwork0.164 ---
all0.165 46672 --
obs0.165 46672 96.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.895 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.7535 Å2-0 Å2-2.0419 Å2
2---2.5596 Å2-0 Å2
3---0.8061 Å2
Refinement stepCycle: LAST / Resolution: 1.493→30.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 130 358 2660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012544
X-RAY DIFFRACTIONf_angle_d1.3093415
X-RAY DIFFRACTIONf_dihedral_angle_d17.3721007
X-RAY DIFFRACTIONf_chiral_restr0.085333
X-RAY DIFFRACTIONf_plane_restr0.005443
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4936-1.52410.27851060.2511969207569
1.5241-1.55720.24191190.23972229234881
1.5572-1.59340.21861430.23772531267489
1.5934-1.63320.28941440.24282617276194
1.6332-1.67730.2531360.22312662279895
1.6773-1.72670.271420.24082663280595
1.7267-1.78230.23811450.24692652299795
1.7823-1.8460.26541530.24152711286495
1.846-1.91980.24511190.23292651277096
1.9198-2.0070.20021570.20922669282694
2.007-2.11270.21361620.20872657281994
2.1127-2.24480.22621180.19062693281196
2.2448-2.41770.20271480.18732698284695
2.4177-2.66020.2091330.17612706283995
2.6602-3.04320.21941360.15682717285395
3.0432-3.82720.16711270.10932733286095
3.8272-17.21440.1311660.10092736290292
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)
10.61980.0075-0.39720.1211-0.15160.6691-0.00260.0565-0.00770.0648-0.00790.03660.0089-0.03080.00410.1363-0.00720.0230.1382-0.00830.146443.216317.62325.1346
20.4901-0.03290.19170.11290.03420.62960.03060.0211-0.03080.0250.0001-0.0337-0.0140.029-0.01660.1254-0.00670.01030.14580.01030.163845.836513.9523-30.3332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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