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- PDB-3iqt: Structure of the HPT domain of Sensor protein barA from Escherich... -

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Basic information

Entry
Database: PDB / ID: 3iqt
TitleStructure of the HPT domain of Sensor protein barA from Escherichia coli CFT073.
ComponentsSignal transduction histidine-protein kinase barA
KeywordsTRANSFERASE / Histidine Phosphotransfer domain / HTP / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Cell inner membrane / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transcription / Transcription regulation / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Histidine kinase BarA, N-terminal / Single cache domain 4 / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain ...Histidine kinase BarA, N-terminal / Single cache domain 4 / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Signal transduction histidine-protein kinase BarA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.4 Å
AuthorsCuff, M.E. / Rakowski, E. / Kim, Y. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the HPT domain of Sensor protein barA from Escherichia coli CFT073.
Authors: Cuff, M.E. / Rakowski, E. / Kim, Y. / Freeman, L. / Joachimiak, A.
History
DepositionAug 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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: Signal transduction histidine-protein kinase barA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1863
Polymers13,9361
Non-polymers2492
Water2,540141
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.316, 60.359, 37.156
Angle α, β, γ (deg.)90.000, 108.210, 90.000
Int Tables number4
Space group name H-MP1211
Detailsauthors state that the biological unit is unknown but likely monomer

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Components

#1: Protein Signal transduction histidine-protein kinase barA


Mass: 13936.207 Da / Num. of mol.: 1 / Fragment: Histidine Phosphotransfer domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: barA, c3349 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0AEC6, histidine kinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.86 Å3/Da / Density % sol: 33.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M Calcium Chloride dihydrate, ).1M Bis Tris pH6.5, 30% PEG Monomethyl ether 550, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Av σ(I) over netI: 24.16 / Number: 99422 / Rmerge(I) obs: 0.094 / Χ2: 2.52 / D res high: 1.4 Å / D res low: 50 Å / Num. obs: 19949 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.85088.310.098.1824.5
3.023.899.110.0725.0424.8
2.633.0299.810.0865.1054.9
2.392.6310010.0864.2945
2.222.3910010.0953.8875.1
2.092.2210010.0933.2885.1
1.992.0910010.13.0195.1
1.91.9910010.1132.7575.1
1.831.910010.1192.3065.1
1.761.8310010.1321.885.1
1.711.7610010.1441.85.1
1.661.7110010.1511.5275.1
1.621.6610010.1651.3435
1.581.6210010.1811.2215
1.541.5810010.21.1075
1.511.5410010.2141.0735
1.481.5110010.2560.9845
1.451.4810010.2890.9295
1.421.4510010.3730.8465
1.41.4210010.4140.9284.9
ReflectionResolution: 1.4→50 Å / Num. all: 19949 / Num. obs: 19949 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.094 / Χ2: 2.515 / Net I/σ(I): 10.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.414 / Num. unique all: 1030 / Χ2: 0.928 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.4 Å / D res low: 35.29 Å / FOM : 0.349 / FOM acentric: 0.361 / FOM centric: 0 / Reflection: 19914 / Reflection acentric: 19248 / Reflection centric: 666
Phasing MAD setR cullis acentric: 1.32 / R cullis centric: 1 / Highest resolution: 1.4 Å / Lowest resolution: 35.29 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 19248 / Reflection centric: 666
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
8.77-35.291.60.40.22610
5-8.771.10.30.230530
3.5-50.960.30.376049
2.69-3.51.160.20.2146973
2.19-2.691.270.20.1235499
1.84-2.191.390.10.13457117
1.59-1.841.790.104718138
1.4-1.591.82006159150
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se22.87614-0.141-0.226-0.3490
2Se16.6292-0.097-0.226-0.1710
3Se15.980780.309-0.292-0.480
4Se17.598680.332-0.273-0.5940
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.77-35.290.2820.3910362610
5-8.770.4260.468033530530
3.5-50.4320.46080976049
2.69-3.50.4980.52301542146973
2.19-2.690.4790.49902453235499
1.84-2.190.460.475035743457117
1.59-1.840.3460.356048564718138
1.4-1.590.1880.192063096159150
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 19914
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
4.56-10061.50.793502
3.67-4.5658.40.904512
3.24-3.6760.60.921512
2.96-3.2460.10.892511
2.75-2.96580.897514
2.59-2.7556.50.91551
2.45-2.5959.50.921551
2.33-2.4556.70.919605
2.23-2.3358.50.91629
2.14-2.2360.60.901668
2.06-2.1458.60.906681
1.99-2.0661.50.896715
1.92-1.9960.10.876738
1.86-1.9259.10.884733
1.81-1.8663.30.865796
1.76-1.8163.30.852799
1.71-1.7664.10.857827
1.67-1.7165.60.846866
1.63-1.6771.10.851842
1.6-1.6369.90.843912
1.56-1.673.50.836908
1.53-1.5673.10.842928
1.5-1.5374.20.84923
1.47-1.578.10.844966
1.44-1.4778.60.828978
1.4-1.4479.80.7621747

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.4→35.3 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.029 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.064
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1012 5.1 %RANDOM
Rwork0.141 ---
all0.143 19928 --
obs0.143 19928 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.63 Å2 / Biso mean: 19.949 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-0.04 Å2
2--0.94 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 15 141 1116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221031
X-RAY DIFFRACTIONr_bond_other_d0.0020.02712
X-RAY DIFFRACTIONr_angle_refined_deg1.4932.0241395
X-RAY DIFFRACTIONr_angle_other_deg0.93131758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.095130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24426.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35915195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.226157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02170
X-RAY DIFFRACTIONr_mcbond_it1.2561.5639
X-RAY DIFFRACTIONr_mcbond_other0.6021.5255
X-RAY DIFFRACTIONr_mcangle_it2.01621031
X-RAY DIFFRACTIONr_scbond_it3.0883392
X-RAY DIFFRACTIONr_scangle_it4.8874.5363
X-RAY DIFFRACTIONr_rigid_bond_restr1.37131743
X-RAY DIFFRACTIONr_sphericity_free5.8193142
X-RAY DIFFRACTIONr_sphericity_bonded3.2831731
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 63 -
Rwork0.162 1424 -
all-1487 -
obs--98.22 %

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