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- PDB-3by9: Crystal structure of the V. cholerae Histidine Kinase DctB Sensor... -

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Basic information

Entry
Database: PDB / ID: 3by9
TitleCrystal structure of the V. cholerae Histidine Kinase DctB Sensor Domain
ComponentsSensor protein
KeywordsTRANSFERASE / histidine kinase sensor domain / Phosphoprotein / Two-component regulatory system
Function / homology
Function and homology information


C4-dicarboxylate transport / histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, DctB (C4-dicarboxylate transport system regulator) / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal ...Signal transduction histidine kinase, DctB (C4-dicarboxylate transport system regulator) / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / Histidine kinase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsCheung, J. / Hendrickson, W.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structures of C4-Dicarboxylate Ligand Complexes with Sensor Domains of Histidine Kinases DcuS and DctB.
Authors: Cheung, J. / Hendrickson, W.A.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3116
Polymers59,9942
Non-polymers3164
Water12,989721
1
A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1954
Polymers29,9971
Non-polymers1983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1152
Polymers29,9971
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.311, 90.982, 114.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sensor protein


Mass: 29997.102 Da / Num. of mol.: 2 / Fragment: residues 28-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC1925 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KQS3, histidine kinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: isopropanol, calcium acetate, pH 7.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9637, 0.9788, 0.9791, 0.9946
DetectorDetector: CCD / Date: Feb 19, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96371
20.97881
30.97911
40.99461
ReflectionAv σ(I) over netI: 15.4 / Number: 284212 / Rmerge(I) obs: 0.061 / Χ2: 1.01 / D res high: 2.2 Å / D res low: 20 Å / Num. obs: 56978 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.722099.910.0411.01
3.764.7210010.0441.026
3.283.7610010.0511.02
2.983.2810010.0621.023
2.772.9810010.0751.04
2.612.7710010.0921.033
2.482.6199.910.1061.027
2.372.4899.410.1160.994
2.282.3797.710.1250.947
2.22.2891.210.1290.914
ReflectionResolution: 1.6→20 Å / Num. obs: 76821 / % possible obs: 98.4 % / Rmerge(I) obs: 0.057 / Χ2: 0.998 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.660.39570890.8391.8
1.66-1.720.31474190.88596.5
1.72-1.80.23776980.96699.7
1.8-1.90.17677071.02299.6
1.9-2.020.12376951.04199.5
2.02-2.170.08977381.03299.6
2.17-2.390.0777481.01899.7
2.39-2.730.05677931.0399.6
2.73-3.440.03978531.04399.4
3.44-200.03280811.0398.6

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Phasing

PhasingMethod: MAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 64840
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.6-10046.30.927506
6.29-8.642.30.936834
5.19-6.2939.20.9381041
4.53-5.1937.90.9491221
4.06-4.5339.20.9431342
3.72-4.0641.40.9361476
3.45-3.7242.10.9241609
3.23-3.4542.60.9181709
3.05-3.2342.70.9161808
2.89-3.0544.30.8991917
2.76-2.8944.50.9092001
2.64-2.7644.20.9072101
2.54-2.6446.80.9042176
2.45-2.5451.70.9012241
2.37-2.4554.30.9082361
2.29-2.3760.20.9142418
2.23-2.2964.60.9052493
2.16-2.2381.20.9022544
2.11-2.1690.70.9082638
2.05-2.1190.20.9042691
2-2.0588.30.9022741
1.96-289.50.8992820
1.92-1.96890.8862926
1.88-1.92910.8852897
1.84-1.88890.8763021
1.8-1.84900.8743059
1.77-1.890.90.8593123
1.74-1.7790.40.8153190
1.7-1.74900.6773936

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DM4.2phasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.78 Å / Rfactor Rfree error: 0.003 / FOM work R set: 0.895 / Data cutoff high absF: 1911155.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.199 3285 5.1 %RANDOM
Rwork0.162 ---
obs-64840 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.92 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å20 Å2
2---2.62 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 18 721 5138
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it2.321.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it3.952
X-RAY DIFFRACTIONc_scangle_it5.432.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 572 5.4 %
Rwork0.189 10058 -
all-10630 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramsin_xplor_top.txt
X-RAY DIFFRACTION3sin_xplor_par.txtwater.top
X-RAY DIFFRACTION4ion.param

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