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- PDB-8f07: Proteinase K Anomalous Dataset at 273 K and 12 keV -

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Basic information

Entry
Database: PDB / ID: 8f07
TitleProteinase K Anomalous Dataset at 273 K and 12 keV
ComponentsProteinase K
KeywordsHYDROLASE / Proteinase K / serine proteases
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 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: 1.05 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 1.1Nov 13, 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)29,86311
Polymers28,9591
Non-polymers90510
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-106 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.382, 68.382, 103.558
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-549-

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.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
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: 273 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.05→35.365 Å / Num. obs: 113400 / % possible obs: 98.9 % / Redundancy: 22.7 % / Biso Wilson estimate: 11.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.014 / Net I/σ(I): 34.5
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 4748 / CC1/2: 0.92 / Rpim(I) all: 0.222 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.05→35.365 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.985 / WRfactor Rfree: 0.102 / WRfactor Rwork: 0.093 / SU B: 0.399 / SU ML: 0.009 / Average fsc free: 0.9941 / Average fsc work: 0.9954 / Cross valid method: FREE R-VALUE / ESU R: 0.018 / ESU R Free: 0.017
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1048 5747 5.072 %
Rwork0.0956 107552 -
all0.096 --
obs-113299 98.851 %
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: 9.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.628 Å2-0 Å2-0 Å2
2--0.628 Å2-0 Å2
3----1.256 Å2
Refinement stepCycle: LAST / Resolution: 1.05→35.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 46 298 2376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161948
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.643156
X-RAY DIFFRACTIONr_angle_other_deg0.5981.5564590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.02515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24110350
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.3271096
X-RAY DIFFRACTIONr_chiral_restr0.0970.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined0.2280.2406
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21769
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21124
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21192
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2157
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.214
X-RAY DIFFRACTIONr_nbd_other0.2160.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2950.233
X-RAY DIFFRACTIONr_mcbond_it0.8360.6161181
X-RAY DIFFRACTIONr_mcbond_other0.80.6151181
X-RAY DIFFRACTIONr_mcangle_it1.0261.1961491
X-RAY DIFFRACTIONr_mcangle_other1.0561.1991492
X-RAY DIFFRACTIONr_scbond_it13.5931.5431105
X-RAY DIFFRACTIONr_scbond_other3.4831.2471070
X-RAY DIFFRACTIONr_scangle_it11.9422.7591637
X-RAY DIFFRACTIONr_scangle_other4.0042.0391584
X-RAY DIFFRACTIONr_lrange_it3.84313.542615
X-RAY DIFFRACTIONr_lrange_other3.4338.852541
X-RAY DIFFRACTIONr_rigid_bond_restr12.32334234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.05-1.0770.1343650.13669360.13683370.9910.9987.57350.112
1.077-1.1070.1113990.10475620.10481680.9920.99497.46570.084
1.107-1.1390.0933840.08575300.08679350.9950.99699.73540.069
1.139-1.1740.0874220.07572530.07676750.9960.9971000.061
1.174-1.2120.0923720.07471070.07574790.9960.9971000.06
1.212-1.2550.0913750.07468830.07572580.9950.9971000.061
1.255-1.3020.0873700.07666140.07769850.9950.99799.98570.063
1.302-1.3550.0893420.07664040.07767460.9960.9971000.064
1.355-1.4150.0893400.07461380.07564780.9950.9971000.063
1.415-1.4840.0893020.07559070.07662090.9950.9971000.065
1.484-1.5650.0992900.07756190.07859090.9940.9971000.07
1.565-1.6590.0962750.08253290.08256050.9950.99699.98220.075
1.659-1.7740.0942670.08450230.08552900.9950.9961000.079
1.774-1.9150.0952470.08746860.08749330.9950.9961000.084
1.915-2.0970.0972360.08543200.08645560.9950.9961000.085
2.097-2.3440.12010.09239510.09241520.9940.9951000.095
2.344-2.7050.1111900.10535010.10636910.9920.9931000.112
2.705-3.3080.1391710.11929810.1231530.9890.99199.96830.133
3.308-4.6570.0961250.11123770.1125020.9940.9931000.128
4.657-35.3650.198740.1814310.18115060.9790.98299.93360.205
Refinement TLS params.Method: refined / Origin x: 52.2432 Å / Origin y: 13.0743 Å / Origin z: 0.2851 Å
111213212223313233
T0.0004 Å20.0005 Å2-0.0026 Å2-0.0015 Å2-0.0006 Å2--0.0694 Å2
L0.6974 °2-0.1064 °20.0435 °2-0.5627 °20.0781 °2--0.4318 °2
S0.0032 Å °0.0274 Å °-0.0125 Å °-0.0031 Å °-0.0043 Å °0.0307 Å °0.0114 Å °0.0146 Å °0.0011 Å °
Refinement TLS groupSelection: ALL

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