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- PDB-4k0d: Periplasmic sensor domain of sensor histidine kinase, Adeh_2942 -

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Basic information

Entry
Database: PDB / ID: 4k0d
TitlePeriplasmic sensor domain of sensor histidine kinase, Adeh_2942
ComponentsPeriplasmic sensor hybrid histidine kinase
KeywordsSIGNALING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helical bundle sensor domain / Periplasmic sensor domain
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1730 / 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 ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1730 / 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
ACETATE ION / Histidine kinase
Similarity search - Component
Biological speciesAnaeromyxobacter dehalogenans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.997 Å
AuthorsPokkuluri, P.R. / Mack, J.C. / Bearden, J. / Rakowski, E. / Schiffer, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Microbiologyopen / Year: 2013
Title: Analysis of periplasmic sensor domains from Anaeromyxobacter dehalogenans 2CP-C: structure of one sensor domain from a histidine kinase and another from a chemotaxis protein.
Authors: Pokkuluri, P.R. / Dwulit-Smith, J. / Duke, N.E. / Wilton, R. / Mack, J.C. / Bearden, J. / Rakowski, E. / Babnigg, G. / Szurmant, H. / Joachimiak, A. / Schiffer, M.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Structure summary
Revision 1.2Apr 15, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic sensor hybrid histidine kinase
B: Periplasmic sensor hybrid histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,06314
Polymers31,4532
Non-polymers61012
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-245 kcal/mol
Surface area12850 Å2
MethodPISA
2
A: Periplasmic sensor hybrid histidine kinase
B: Periplasmic sensor hybrid histidine kinase
hetero molecules

A: Periplasmic sensor hybrid histidine kinase
B: Periplasmic sensor hybrid histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,12628
Polymers62,9064
Non-polymers1,22024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area11290 Å2
ΔGint-546 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.693, 75.184, 51.031
Angle α, β, γ (deg.)90.00, 105.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Periplasmic sensor hybrid histidine kinase


Mass: 15726.584 Da / Num. of mol.: 2 / Fragment: Periplasmic sensor domain (UNP residues 33-184)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaeromyxobacter dehalogenans (bacteria)
Strain: 2CP-C / Gene: Adeh_2942 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IDQ5

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Non-polymers , 5 types, 223 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Wizard II no.11 (10% 2-propanol, 0.1 M sodium cacodylate pH 6.5, 0.2 M zinc acetate), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorDetector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 37922 / % possible obs: 89.9 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 18
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / Num. unique all: 1313 / % possible all: 62.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.997→29.882 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.94 / Phase error: 29.41 / Stereochemistry target values: ML / Details: Hydrogens were added in riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1940 5.14 %random
Rwork0.198 ---
obs0.2006 37771 88.41 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.141 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7208 Å20 Å2-14.6705 Å2
2---18.0991 Å2-0 Å2
3---17.3784 Å2
Refinement stepCycle: LAST / Resolution: 1.997→29.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 18 211 2254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182102
X-RAY DIFFRACTIONf_angle_d1.6572869
X-RAY DIFFRACTIONf_dihedral_angle_d14.935747
X-RAY DIFFRACTIONf_chiral_restr0.082346
X-RAY DIFFRACTIONf_plane_restr0.009384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9969-2.06830.38051350.27272297X-RAY DIFFRACTION57
2.0683-2.15110.33181510.25533105X-RAY DIFFRACTION76
2.1511-2.24890.32381790.23683288X-RAY DIFFRACTION83
2.2489-2.36750.27221960.21893586X-RAY DIFFRACTION89
2.3675-2.51570.26681930.23133822X-RAY DIFFRACTION94
2.5157-2.70980.32672290.22243811X-RAY DIFFRACTION95
2.7098-2.98230.24212040.19863918X-RAY DIFFRACTION96
2.9823-3.41330.23512120.194021X-RAY DIFFRACTION99
3.4133-4.29840.21692200.16874007X-RAY DIFFRACTION99
4.2984-29.88550.22072210.1843976X-RAY DIFFRACTION98

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