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- PDB-3lic: Crystal Structure of the extracellular domain of the putative his... -

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Basic information

Entry
Database: PDB / ID: 3lic
TitleCrystal Structure of the extracellular domain of the putative histidine kinase soHK1S-Z6
ComponentsSensor protein
KeywordsSIGNALING PROTEIN / PDC fold / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Transferase / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / PAS fold-3 / PAS fold / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAC domain profile. ...Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / PAS fold-3 / PAS fold / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAC domain profile. / PAS domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsZhang, Z. / Hendrickson, W.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural characterization of the predominant family of histidine kinase sensor domains.
Authors: Zhang, Z. / Hendrickson, W.A.
History
DepositionJan 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7042
Polymers30,6421
Non-polymers621
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sensor protein
hetero molecules

A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4084
Polymers61,2842
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area2300 Å2
ΔGint-6 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.069, 133.069, 32.369
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Sensor protein / / Sensory box histidine kinase/response regulator


Mass: 30642.025 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 36-308)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_0859 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EII0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.8
Details: 5% PEG3350, 0.5M NH4SO4, 0.1M Na Citrate pH 5.8, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97927, 0.97937, 0.96789
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979371
30.967891
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 28.58 / Number: 196577 / Rmerge(I) obs: 0.068 / Χ2: 1.01 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 28506 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955099.710.0470.9767.1
3.934.9510010.0471.0097.1
3.443.9310010.0530.9997.1
3.123.4410010.0650.9937.2
2.93.1210010.0811.0447.2
2.732.910010.1061.0187
2.592.7310010.1340.9896.9
2.482.5910010.1661.056.7
2.382.4810010.1961.0226.4
2.32.3810010.2251.0416.3
ReflectionResolution: 2.3→50 Å / Num. obs: 28506 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.068 / Χ2: 1.013 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.386.30.22528231.041100
2.38-2.486.40.19628841.022100
2.48-2.596.70.16628191.05100
2.59-2.736.90.13428730.989100
2.73-2.970.10628571.018100
2.9-3.127.20.08128281.044100
3.12-3.447.20.06528660.993100
3.44-3.937.10.05328570.999100
3.93-4.957.10.04728261.009100
4.95-507.10.04728730.97699.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.3→38.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.043 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 745 5 %RANDOM
Rwork0.181 ---
obs0.184 14789 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 74.1 Å2 / Biso mean: 27.186 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å20 Å2
2--0.61 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 4 111 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222171
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9442948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4775267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18324.579107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89515351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1411510
X-RAY DIFFRACTIONr_chiral_restr0.1520.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211681
X-RAY DIFFRACTIONr_mcbond_it1.2181.51320
X-RAY DIFFRACTIONr_mcangle_it2.22922115
X-RAY DIFFRACTIONr_scbond_it3.3973851
X-RAY DIFFRACTIONr_scangle_it5.3254.5831
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 46 -
Rwork0.178 1031 -
all-1077 -
obs--100 %

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