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- PDB-8rsf: Proteinase K measured via serial crystallography from a kapton HA... -

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Basic information

Entry
Database: PDB / ID: 8rsf
TitleProteinase K measured via serial crystallography from a kapton HARE-chip (50 micron)
ComponentsProteinase K
KeywordsHYDROLASE / Proteianse K / Serine Protease
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. ...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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsBosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Schulz, E.C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Economic Affairs and Energy01KI2114 Germany
CitationJournal: To Be Published
Title: Kapton-based HARE chips for fixed-target serial crystallography
Authors: Bosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Blatter, G. / Lu, G. / Bernhard, S. / Osbild, M. / Schulz, E.C.
History
DepositionJan 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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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)40,4673
Polymers40,3651
Non-polymers1022
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-10 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.500, 68.500, 108.750
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-452-

HOH

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Components

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


Mass: 40364.902 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 137 / 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

Crystal growTemperature: 293 K / Method: batch mode
Details: Microcrystals were obtained by mixing proteinase K solution (60mg/ml) with precipitant solution 1M NaNO3, 0.1M sodium citrate pH 6.5, in a 5:1 ratio and left overnight at room temperature.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.66→57.96 Å / Num. obs: 32794 / % possible obs: 100 % / Redundancy: 889.4 % / Biso Wilson estimate: 10.37 Å2 / CC1/2: 0.991 / R split: 0.998 / Net I/σ(I): 17.29
Reflection shellResolution: 1.66→1.73 Å / Mean I/σ(I) obs: 11.34 / Num. unique obs: 2605 / CC1/2: 0.993 / R split: 0.0946
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: HARE-Chip , Kapton (50um)

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFEL0.10.2data reduction
CrystFEL0.10.2data scaling
PHENIX2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→57.96 Å / SU ML: 0.1106 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.7743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1579 1552 4.95 %
Rwork0.133 29770 -
obs0.1342 31322 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.37 Å2
Refinement stepCycle: LAST / Resolution: 1.66→57.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 5 137 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01162251
X-RAY DIFFRACTIONf_angle_d1.09853087
X-RAY DIFFRACTIONf_chiral_restr0.078337
X-RAY DIFFRACTIONf_plane_restr0.0112420
X-RAY DIFFRACTIONf_dihedral_angle_d5.7968350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.710.16521490.13152655X-RAY DIFFRACTION99.96
1.71-1.770.14761200.11282656X-RAY DIFFRACTION99.93
1.77-1.850.1481340.11982680X-RAY DIFFRACTION99.96
1.85-1.930.16061330.1262639X-RAY DIFFRACTION100
1.93-2.030.16271480.13032672X-RAY DIFFRACTION99.93
2.03-2.160.14511580.12952662X-RAY DIFFRACTION99.96
2.16-2.330.17961360.13512687X-RAY DIFFRACTION100
2.33-2.560.17261380.15282711X-RAY DIFFRACTION100
2.56-2.930.18711430.15012726X-RAY DIFFRACTION100
2.93-3.690.14221320.13722771X-RAY DIFFRACTION100
3.69-57.960.1421610.12172911X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: 50.9340577314 Å / Origin y: 46.8708273934 Å / Origin z: 27.569437944 Å
111213212223313233
T0.0597950533278 Å2-0.00146226594054 Å2-0.0069990483633 Å2-0.042555364575 Å2-0.000251770173413 Å2--0.0503795581491 Å2
L0.778932882329 °20.174555618262 °2-0.00472429735265 °2-0.87681878493 °20.0550529262532 °2--0.524742812856 °2
S-0.00463650195456 Å °-0.0250414575749 Å °0.00110108542503 Å °-0.0396978824633 Å °0.0023861271351 Å °-0.0532090562032 Å °-0.0182691140077 Å °-0.00953878603178 Å °0.00294236264812 Å °
Refinement TLS groupSelection details: all

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