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- PDB-5wrc: Crystal structure of proteinase K from Engyodontium album -

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Basic information

Entry
Database: PDB / ID: 5wrc
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 / PRASEODYMIUM ION / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 1.5 Å
AuthorsSugahara, M. / Nakane, T. / Suzuki, M. / Masuda, T. / Inoue, S. / Numata, K.
CitationJournal: Sci Rep / Year: 2017
Title: Hydroxyethyl cellulose matrix applied to serial crystallography
Authors: Sugahara, M. / Nakane, T. / Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Tanaka, R. / Nakatsu, T. / Mizohata, E. / Yumoto, F. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / ...Authors: Sugahara, M. / Nakane, T. / Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Tanaka, R. / Nakatsu, T. / Mizohata, E. / Yumoto, F. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Nureki, O. / Numata, K. / Nango, E. / Iwata, S.
History
DepositionDec 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 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)29,3034
Polymers28,9591
Non-polymers3443
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-15 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.600, 68.600, 108.800
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-1182-

HOH

21A-1303-

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.) Engyodontium album (fungus) / Gene: PROK / Production host: Engyodontium 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-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 291 K / Method: batch mode / Details: NaNO3

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Data collection

DiffractionMean temperature: 299 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.5→32.7 Å / Num. obs: 42391 / % possible obs: 100 % / Redundancy: 400 % / Net I/σ(I): 10.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
CrystFELdata processing
CrystFELdata scaling
Cootmodel building
RefinementResolution: 1.5→32.7 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.68
RfactorNum. reflection% reflection
Rfree0.1926 1398 3.3 %
Rwork0.1762 --
obs0.1767 42306 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 6 215 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092075
X-RAY DIFFRACTIONf_angle_d1.0042816
X-RAY DIFFRACTIONf_dihedral_angle_d12.252717
X-RAY DIFFRACTIONf_chiral_restr0.041312
X-RAY DIFFRACTIONf_plane_restr0.005372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.55360.3051370.2234028X-RAY DIFFRACTION100
1.5536-1.61580.21191370.18784001X-RAY DIFFRACTION100
1.6158-1.68940.20611380.18174034X-RAY DIFFRACTION100
1.6894-1.77840.19461380.16734028X-RAY DIFFRACTION100
1.7784-1.88990.18451380.16554047X-RAY DIFFRACTION100
1.8899-2.03580.14621390.15894061X-RAY DIFFRACTION100
2.0358-2.24060.19941400.16534081X-RAY DIFFRACTION100
2.2406-2.56470.1821400.17124106X-RAY DIFFRACTION100
2.5647-3.23080.20321430.17514160X-RAY DIFFRACTION100
3.2308-32.72060.19161480.18884362X-RAY DIFFRACTION100

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