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- PDB-9kw1: Crystal structure of proteinase K from Engyodontium album -

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Basic information

Entry
Database: PDB / ID: 9kw1
TitleCrystal structure of proteinase K from Engyodontium album
ComponentsProteinase K
KeywordsHYDROLASE / Engyodontium album
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, 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
EUROPIUM ION / NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 1.2 Å
AuthorsSugahara, M. / Maki-Yonekura, S. / Yonekura, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of proteinase K from Engyodontium album
Authors: Sugahara, M. / Maki-Yonekura, S. / Yonekura, K.
History
DepositionDec 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: 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)29,3254
Polymers28,9591
Non-polymers3663
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-8 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.700, 68.700, 108.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1198-

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-EU / EUROPIUM ION


Mass: 151.964 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Eu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 0.5 M NaNO3, 0.1 M CaCl2, 0.1 M MES

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 0.827 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.2→29.6 Å / Num. obs: 82104 / % possible obs: 100 % / Redundancy: 265 % / CC1/2: 0.94 / Net I/σ(I): 6
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 4018 / CC1/2: 0.472
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrystFELdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→20.19 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1825 4100 5.01 %
Rwork0.1691 --
obs0.1698 81908 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→20.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 6 248 2285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.439307
X-RAY DIFFRACTIONf_chiral_restr0.081312
X-RAY DIFFRACTIONf_plane_restr0.007372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.34751250.32992645X-RAY DIFFRACTION100
1.21-1.230.30911350.31072662X-RAY DIFFRACTION100
1.23-1.240.31981390.28622611X-RAY DIFFRACTION100
1.24-1.260.26731350.27482631X-RAY DIFFRACTION100
1.26-1.280.26271560.25562652X-RAY DIFFRACTION100
1.28-1.30.24651200.23212668X-RAY DIFFRACTION100
1.3-1.320.2631460.22542642X-RAY DIFFRACTION100
1.32-1.340.20271270.21342642X-RAY DIFFRACTION100
1.34-1.360.21791400.20762677X-RAY DIFFRACTION100
1.36-1.380.21121520.20592626X-RAY DIFFRACTION100
1.38-1.410.18691420.20852657X-RAY DIFFRACTION100
1.41-1.430.18221370.20642669X-RAY DIFFRACTION100
1.43-1.460.16481600.18072638X-RAY DIFFRACTION100
1.46-1.490.18721390.16672678X-RAY DIFFRACTION100
1.49-1.530.16711280.16052667X-RAY DIFFRACTION100
1.53-1.570.17231280.15792682X-RAY DIFFRACTION100
1.57-1.610.17711610.15492637X-RAY DIFFRACTION100
1.61-1.660.16131370.15782669X-RAY DIFFRACTION100
1.66-1.710.17151440.15642679X-RAY DIFFRACTION100
1.71-1.770.17351450.15482671X-RAY DIFFRACTION100
1.77-1.840.19731430.1562698X-RAY DIFFRACTION100
1.84-1.930.17371450.14852685X-RAY DIFFRACTION100
1.93-2.030.15681440.15122699X-RAY DIFFRACTION100
2.03-2.160.17091460.15432704X-RAY DIFFRACTION100
2.16-2.320.18161670.15672695X-RAY DIFFRACTION100
2.32-2.550.18931400.16832742X-RAY DIFFRACTION100
2.55-2.920.18261350.17342758X-RAY DIFFRACTION100
2.92-3.680.17941420.1562795X-RAY DIFFRACTION100
3.68-20.190.15621420.15112929X-RAY DIFFRACTION99

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