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- PDB-2r78: Crystal structure of a domain of the sensory box sensor histidine... -

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Basic information

Entry
Database: PDB / ID: 2r78
TitleCrystal structure of a domain of the sensory box sensor histidine kinase/response regulator from Geobacter sulfurreducens
ComponentsSensor protein
KeywordsTRANSFERASE / sensory box sensor histidine kinase/response regulator / Structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Phosphorylation
Function / homology
Function and homology information


protein histidine kinase activity / histidine phosphotransfer kinase activity / histidine kinase / plasma membrane => GO:0005886 / phosphorelay sensor kinase activity / protein autophosphorylation
Similarity search - Function
PAS fold-4 / PAS fold / HPT 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 ...PAS fold-4 / PAS fold / HPT 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. / Response regulator receiver domain / cheY-homologous 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 / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Histidine kinase
Similarity search - Component
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain of the sensory box sensor histidine kinase/response regulator from Geobacter sulfurreducens.
Authors: Zhang, R. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: 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: Sensor protein
B: Sensor protein
C: Sensor protein
D: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,11114
Polymers51,5214
Non-polymers59010
Water8,701483
1
A: Sensor protein
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0567
Polymers25,7602
Non-polymers2955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
MethodPISA
2
C: Sensor protein
D: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0567
Polymers25,7602
Non-polymers2955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.248, 62.501, 71.203
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that this protein exists as dimer. MolA/MolB and MolC/MolD represent two dimers in the asymmetric unit.

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Components

#1: Protein
Sensor protein


Mass: 12880.233 Da / Num. of mol.: 4 / Fragment: Domain: Residues 41-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Species: Geobacter sulfurreducens / Strain: PCA, DSM 12127 / Gene: GSU1285 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q74DN1, histidine kinase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Bis-Tris, 25% PEG 3350, pH 5.5, 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: 0.9794 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 21, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→70.89 Å / Num. all: 55965 / Num. obs: 55938 / % possible obs: 99.51 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 17.65 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 31.36
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.73 / Num. unique all: 4330 / % possible all: 95.59

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→70.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.936 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.097
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22098 2979 5.1 %RANDOM
Rwork0.17906 ---
all0.1812 55938 --
obs0.1812 55938 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.515 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.44 Å2
2---0.56 Å20 Å2
3---0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.045 Å0.035 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 1.6→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 40 483 4088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213671
X-RAY DIFFRACTIONr_bond_other_d0.0010.022398
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9494979
X-RAY DIFFRACTIONr_angle_other_deg0.92935781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95723.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23115557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7581532
X-RAY DIFFRACTIONr_chiral_restr0.090.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
X-RAY DIFFRACTIONr_nbd_refined0.230.2807
X-RAY DIFFRACTIONr_nbd_other0.2050.22598
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21785
X-RAY DIFFRACTIONr_nbtor_other0.0870.21915
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2361
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.241
X-RAY DIFFRACTIONr_mcbond_it1.5991.52753
X-RAY DIFFRACTIONr_mcbond_other0.5151.5952
X-RAY DIFFRACTIONr_mcangle_it1.96623607
X-RAY DIFFRACTIONr_scbond_it2.81931580
X-RAY DIFFRACTIONr_scangle_it4.0144.51372
X-RAY DIFFRACTIONr_rigid_bond_restr1.78237402
X-RAY DIFFRACTIONr_sphericity_free6.5963485
X-RAY DIFFRACTIONr_sphericity_bonded2.80136003
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 209 -
Rwork0.279 3930 -
obs-4139 95.59 %

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