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- PDB-8spl: Proteinase K Multiconformer Model at 343K -

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Basic information

Entry
Database: PDB / ID: 8spl
TitleProteinase K Multiconformer Model at 343K
Components
  • ALA-ALA-ALA-SER-VAL-LYS
  • Proteinase K
KeywordsHYDROLASE / serine hydrolase / subtilisin-like / metal ion binding / a/b three-layered sandwiches
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic 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 ...Proteinase K-like catalytic 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
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsDu, S. / Wankowicz, S. / Yabukarski, F. / Doukov, T. / Herschlag, D. / Fraser, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145238 United States
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Methods Enzymol. / Year: 2023
Title: Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.
Authors: Du, S. / Wankowicz, S.A. / Yabukarski, F. / Doukov, T. / Herschlag, D. / Fraser, J.S.
History
DepositionMay 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase K
B: ALA-ALA-ALA-SER-VAL-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8346
Polymers29,5052
Non-polymers3284
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-46 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.403, 68.403, 104.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

21A-519-

HOH

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Components

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


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Protein/peptide ALA-ALA-ALA-SER-VAL-LYS


Mass: 546.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Proteinase K was dissolved at pH 7.5 to 30 mg/mL in a 50 mM TRIS buffer . The protein was crystallized using a hanging drop setup on a 24 well VDX plate with sealant and 22 mm thick ...Details: Proteinase K was dissolved at pH 7.5 to 30 mg/mL in a 50 mM TRIS buffer . The protein was crystallized using a hanging drop setup on a 24 well VDX plate with sealant and 22 mm thick siliconized circle cover slides by mixing equal amounts of protein solution with ammonium sulfate.

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Data collection

DiffractionMean temperature: 343 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.03316 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.21→35.43 Å / Num. obs: 74345 / % possible obs: 97.43 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.76 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 12.72
Reflection shellResolution: 1.21→1.254 Å / Redundancy: 6 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 7072 / CC1/2: 0.339 / CC star: 0.711 / % possible all: 94.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→35.43 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 1998 2.71 %
Rwork0.1745 71825 -
obs0.1754 73823 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.71 Å2
Refinement stepCycle: LAST / Resolution: 1.21→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 16 127 2213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00397694
X-RAY DIFFRACTIONf_angle_d0.663110559
X-RAY DIFFRACTIONf_chiral_restr0.06231181
X-RAY DIFFRACTIONf_plane_restr0.00551406
X-RAY DIFFRACTIONf_dihedral_angle_d11.66992648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.240.41891360.38874862X-RAY DIFFRACTION93.84
1.24-1.270.40321400.3565045X-RAY DIFFRACTION97.43
1.27-1.310.38191420.33335101X-RAY DIFFRACTION97.71
1.31-1.350.32751400.2915035X-RAY DIFFRACTION97.29
1.35-1.40.29721450.26385206X-RAY DIFFRACTION99.89
1.4-1.460.281440.24875175X-RAY DIFFRACTION99.81
1.46-1.520.25451450.21875219X-RAY DIFFRACTION99.91
1.52-1.610.25441450.20015198X-RAY DIFFRACTION99.65
1.61-1.710.24281450.19095204X-RAY DIFFRACTION98.96
1.71-1.840.20681410.16815069X-RAY DIFFRACTION96.64
1.84-2.020.19351450.15015228X-RAY DIFFRACTION98.79
2.02-2.320.17771430.13985183X-RAY DIFFRACTION97.55
2.32-2.920.17581440.14185167X-RAY DIFFRACTION96.18
2.92-35.430.1421430.12515133X-RAY DIFFRACTION90.98

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