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- PDB-6k2p: Crystal structure of proteinase K from Engyodontium album -

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Basic information

Entry
Database: PDB / ID: 6k2p
TitleCrystal structure of proteinase K from Engyodontium album
ComponentsProteinase K
KeywordsHYDROLASE / XFEL / SFX
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/S53 domain / : / 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 ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / 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 / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSugahara, M. / Motomura, K. / Numata, K.
CitationJournal: To Be Published
Title: Crystal structure of proteinase K from Engyodontium album
Authors: Sugahara, M. / Motomura, K. / Numata, K.
History
DepositionMay 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)29,1014
Polymers28,9591
Non-polymers1423
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.270, 68.270, 108.220
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-1167-

HOH

21A-1296-

HOH

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Components

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


Mass: 28958.791 Da / Num. of mol.: 1 / Mutation: S312D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NO3 / NITRATE ION


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


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5 / 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: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Jan 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.6→32.6 Å / Num. obs: 34559 / % possible obs: 100 % / Redundancy: 315 % / Net I/σ(I): 7.7
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 1695
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Cootmodel building
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→32.554 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.06
RfactorNum. reflection% reflection
Rfree0.1815 1664 4.83 %
Rwork0.1616 --
obs0.1626 34480 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→32.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 6 205 2242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062075
X-RAY DIFFRACTIONf_angle_d1.0152816
X-RAY DIFFRACTIONf_dihedral_angle_d12.228717
X-RAY DIFFRACTIONf_chiral_restr0.043312
X-RAY DIFFRACTIONf_plane_restr0.004372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64710.45031320.43132671X-RAY DIFFRACTION100
1.6471-1.70030.32651350.28982693X-RAY DIFFRACTION100
1.7003-1.76110.25691480.20972668X-RAY DIFFRACTION100
1.7611-1.83160.21561340.18752701X-RAY DIFFRACTION100
1.8316-1.91490.2181420.17242685X-RAY DIFFRACTION100
1.9149-2.01580.19511350.16792714X-RAY DIFFRACTION100
2.0158-2.14210.17391340.1552715X-RAY DIFFRACTION100
2.1421-2.30750.19561360.14942725X-RAY DIFFRACTION100
2.3075-2.53960.16191320.15842744X-RAY DIFFRACTION100
2.5396-2.90690.19131590.16252743X-RAY DIFFRACTION100
2.9069-3.66160.15241310.14592800X-RAY DIFFRACTION100
3.6616-32.56070.14671460.13732957X-RAY DIFFRACTION100

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