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- PDB-3li9: Crystal Structure of the extracellular domain of the putative his... -

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Basic information

Entry
Database: PDB / ID: 3li9
TitleCrystal Structure of the extracellular domain of the putative histidine kinase mmHK1S-Z2
ComponentsHypothetical sensory transduction histidine kinase
KeywordsSIGNALING PROTEIN / PDC fold
Function / homology
Function and homology information


protein histidine kinase activity / histidine kinase / signal transduction / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, subgroup 2, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / Double Cache domain 1 / Cache domain / PAS fold-3 / PAS fold / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain ...Signal transduction histidine kinase, subgroup 2, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / Double Cache domain 1 / Cache domain / PAS fold-3 / PAS fold / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS repeat profile. / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 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: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3272
Polymers33,1181
Non-polymers2091
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical sensory transduction histidine kinase
hetero molecules

A: Hypothetical sensory transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6544
Polymers66,2352
Non-polymers4182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4160 Å2
ΔGint-2 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.283, 88.495, 99.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hypothetical sensory transduction histidine kinase


Mass: 33117.594 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 32-313)
Source method: isolated from a genetically manipulated source
Details: ATCC BAA-159D / Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: DSM 3647 / Gene: MM_2955 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PSW8
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


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


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 15% PEG3350, 0.21M NH4SO4, 0.1MBistris, pH 5.6, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97903, 0.97936, 0.97174
DetectorDetector: CCD / Date: Aug 2, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.979361
30.971741
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 29.56 / Number: 286446 / Rmerge(I) obs: 0.048 / Χ2: 1.01 / D res high: 1.7 Å / D res low: 20 Å / Num. obs: 62000 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.662094.610.0321.0294.8
2.93.6697.910.0351.0044.8
2.542.998.110.0441.0414.8
2.312.549910.0541.0064.8
2.142.3199.310.0681.0054.8
2.022.1499.810.0881.0424.8
1.912.0299.810.1191.0144.8
1.831.9110010.1680.9974.8
1.761.8399.810.2170.9994.3
1.71.7693.510.2570.9743.5
ReflectionResolution: 1.7→20 Å / Num. obs: 62673 / % possible obs: 98.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.051 / Χ2: 1.014 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.763.50.33558851.00393.2
1.76-1.834.30.27763301.01299.9
1.83-1.914.80.21263621.03100
1.91-2.024.80.14663281.025100
2.02-2.144.80.10363411100
2.14-2.314.80.07763210.998100
2.31-2.544.90.0663541.03699.8
2.54-2.94.90.04763071.00599.6
2.9-3.664.90.03562891.0199.3
3.66-204.80.03261561.01996.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.912 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.887 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1668 5.1 %RANDOM
Rwork0.181 ---
obs0.182 32966 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.71 Å2 / Biso mean: 22.813 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2---0.74 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 14 230 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222124
X-RAY DIFFRACTIONr_angle_refined_deg2.0791.9662879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65625.196102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.595157
X-RAY DIFFRACTIONr_chiral_restr0.1570.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211639
X-RAY DIFFRACTIONr_mcbond_it1.3871.51303
X-RAY DIFFRACTIONr_mcangle_it2.37422109
X-RAY DIFFRACTIONr_scbond_it3.9553821
X-RAY DIFFRACTIONr_scangle_it5.9724.5770
LS refinement shellResolution: 1.695→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 99 -
Rwork0.233 2159 -
all-2258 -
obs--93 %

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