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- PDB-6fjs: Proteinase~K SIRAS phased structure of room-temperature, serially... -

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Basic information

Entry
Database: PDB / ID: 6fjs
TitleProteinase~K SIRAS phased structure of room-temperature, serially collected synchrotron data
ComponentsProteinase K
KeywordsHYDROLASE / Protease / Serine protease
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsBotha, S. / Baitan, D. / Jungnickel, K.E.J. / Oberthuer, D. / Schmidt, C. / Stern, S. / Wiedorn, M.O. / Perbandt, M. / Chapman, H.N. / Betzel, C.
CitationJournal: IUCrJ / Year: 2018
Title: De novoprotein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography.
Authors: Botha, S. / Baitan, D. / Jungnickel, K.E.J. / Oberthur, D. / Schmidt, C. / Stern, S. / Wiedorn, M.O. / Perbandt, M. / Chapman, H.N. / Betzel, C.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0153
Polymers28,9351
Non-polymers802
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-20 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.550, 67.550, 107.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

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Components

#1: Protein Proteinase K / / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28934.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 50 mM Tris-HCl pH 7.0 with 10 mM CaCl2, 0.6 M NaNO3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→57.18 Å / Num. obs: 37456 / % possible obs: 99.9 % / Redundancy: 214.6 % / Net I/σ(I): 1.99
Reflection shellResolution: 1.9→1.93 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→57.18 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.642 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.112
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1714 992 4.9 %RANDOM
Rwork0.1423 ---
obs0.1438 19280 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.27 Å2 / Biso mean: 16.548 Å2 / Biso min: 7.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.9→57.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 2 120 2153
Biso mean--24.99 26.07 -
Num. residues----279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192124
X-RAY DIFFRACTIONr_bond_other_d0.0020.021899
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9332896
X-RAY DIFFRACTIONr_angle_other_deg1.07534370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21323.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36515307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7641512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022550
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02506
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 83 -
Rwork0.2 1382 -
all-1465 -
obs--99.59 %

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