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- PDB-8f06: Proteinase K Anomalous Dataset at 310 K and 7.1 keV -

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Basic information

Entry
Database: PDB / ID: 8f06
TitleProteinase K Anomalous Dataset at 310 K and 7.1 keV
ComponentsProteinase K
KeywordsHYDROLASE / Proteinase K / serine proteases
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/S53 domain / : / 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 ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / 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 / SAD / Resolution: 1.8 Å
AuthorsDoukov, T. / Yabukarski, F. / Herschlag, D.
Funding support United States, France, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
Human Frontier Science Program (HFSP) France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures.
Authors: Doukov, T. / Herschlag, D. / Yabukarski, F.
History
DepositionNov 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2875
Polymers28,9591
Non-polymers3284
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-44 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.950, 67.950, 102.385
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-518-

HOH

21A-624-

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 genetically manipulated source
Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 uL 1 M ammonium sulfate + 2 uL 10 mg/mL proteinase K in 50 mM Tris, pH 7.5

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Data collection

DiffractionMean temperature: 310 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.7462 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 19, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7462 Å / Relative weight: 1
ReflectionResolution: 1.8→35.03 Å / Num. obs: 22689 / % possible obs: 98.8 % / Redundancy: 14.4 % / Biso Wilson estimate: 25.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.022 / Net I/σ(I): 25.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1158 / CC1/2: 0.886 / Rsym value: 0.221 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.03 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.716 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1472 1140 5.041 %
Rwork0.1163 21473 -
all0.118 --
obs-22613 98.618 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.151 Å2
Baniso -1Baniso -2Baniso -3
1--0.609 Å20 Å20 Å2
2---0.609 Å20 Å2
3---1.218 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 16 240 2288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0112202
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161882
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6373027
X-RAY DIFFRACTIONr_angle_other_deg0.5511.554422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.465319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.3021015
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27210331
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.9281093
X-RAY DIFFRACTIONr_chiral_restr0.0780.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_nbd_refined0.2250.2396
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.21737
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21101
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2171
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3610.221
X-RAY DIFFRACTIONr_nbd_other0.2510.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3270.234
X-RAY DIFFRACTIONr_mcbond_it1.6932.1791157
X-RAY DIFFRACTIONr_mcbond_other1.662.1781157
X-RAY DIFFRACTIONr_mcangle_it2.1084.0591455
X-RAY DIFFRACTIONr_mcangle_other2.134.0671456
X-RAY DIFFRACTIONr_scbond_it4.5342.9911045
X-RAY DIFFRACTIONr_scbond_other3.9992.9221034
X-RAY DIFFRACTIONr_scangle_it6.1935.2781551
X-RAY DIFFRACTIONr_scangle_other5.5485.1161534
X-RAY DIFFRACTIONr_lrange_it7.69825.5912565
X-RAY DIFFRACTIONr_lrange_other7.54521.7472504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.346690.2441380X-RAY DIFFRACTION86.8705
1.847-1.8970.206730.1651474X-RAY DIFFRACTION96.0273
1.897-1.9520.168780.1211497X-RAY DIFFRACTION99.8099
1.952-2.0120.153810.1061437X-RAY DIFFRACTION99.9342
2.012-2.0780.126780.0971398X-RAY DIFFRACTION99.5951
2.078-2.150.138640.111365X-RAY DIFFRACTION99.8602
2.15-2.2310.161660.1151330X-RAY DIFFRACTION99.8569
2.231-2.3220.184670.1191266X-RAY DIFFRACTION99.925
2.322-2.4240.179720.121222X-RAY DIFFRACTION99.9228
2.424-2.5420.145590.111166X-RAY DIFFRACTION99.837
2.542-2.6790.14640.1031121X-RAY DIFFRACTION99.8315
2.679-2.840.143620.1081063X-RAY DIFFRACTION99.9112
2.84-3.0350.183520.123991X-RAY DIFFRACTION99.8086
3.035-3.2760.155560.119947X-RAY DIFFRACTION99.9004
3.276-3.5860.127350.111887X-RAY DIFFRACTION100
3.586-4.0040.1460.092796X-RAY DIFFRACTION100
4.004-4.6130.08440.087699X-RAY DIFFRACTION100
4.613-5.6260.149320.099618X-RAY DIFFRACTION99.5406
5.626-7.8550.134230.145498X-RAY DIFFRACTION100
7.855-35.030.174190.175318X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.105 Å / Origin y: 12.9582 Å / Origin z: 25.2854 Å
111213212223313233
T0.0114 Å20.0015 Å2-0.0013 Å2-0.001 Å20.0009 Å2--0.0021 Å2
L1.1132 °20.0703 °20.0127 °2-0.8703 °2-0.0533 °2--0.6416 °2
S0.007 Å °-0.0244 Å °-0.0367 Å °-0.0061 Å °-0.012 Å °-0.0277 Å °0.0172 Å °-0.0048 Å °0.005 Å °
Refinement TLS groupSelection: ALL

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