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- PDB-6j43: Proteinase K determined by PAL-XFEL -

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Basic information

Entry
Database: PDB / ID: 6j43
TitleProteinase K determined by PAL-XFEL
ComponentsProteinase K
KeywordsHYDROLASE / Serine proteiase / XFEL / room temperature
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/S53 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 ...Proteinase K-like catalytic domain / Peptidase S8/S53 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLee, S.J. / Park, J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017M3A9F6029733 Korea, Republic Of
National Research Foundation (Korea)NRF-2016R1C1B2014609 Korea, Republic Of
National Research Foundation (Korea)NRF-2017R1D1A1B03028119 Korea, Republic Of
CitationJournal: J.Appl.Crystallogr. / Year: 2020
Title: Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography.
Authors: Lee, D. / Park, S. / Lee, K. / Kim, J. / Park, G. / Nam, K.H. / Baek, S. / Chung, W.K. / Lee, J.L. / Cho, Y. / Park, J.
History
DepositionJan 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,0393
Polymers28,9591
Non-polymers802
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.540, 68.540, 108.380
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-513-

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: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291 K / Method: batch mode
Details: 0.25 M sodium nitrate, 0.05 M calcium chloride, 0.1 M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.28 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 42177 / % possible obs: 100 % / Redundancy: 6337 % / CC1/2: 0.9939 / R split: 0.0967 / Net I/σ(I): 9.4
Reflection shellResolution: 1.85→1.88 Å / CC1/2: 0.9658 / R split: 0.2614

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B5L

4b5l


Resolution: 1.85→29.495 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 2105 5 %
Rwork0.1961 --
obs0.1983 42112 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→29.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 2 207 2241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062099
X-RAY DIFFRACTIONf_angle_d0.7642864
X-RAY DIFFRACTIONf_dihedral_angle_d2.7031644
X-RAY DIFFRACTIONf_chiral_restr0.052318
X-RAY DIFFRACTIONf_plane_restr0.005379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8930.39211370.32962671X-RAY DIFFRACTION100
1.893-1.94040.23361470.20242694X-RAY DIFFRACTION100
1.9404-1.99280.26681360.21472637X-RAY DIFFRACTION100
1.9928-2.05140.2241400.18952630X-RAY DIFFRACTION100
2.0514-2.11760.25891400.17192690X-RAY DIFFRACTION100
2.1176-2.19330.22451450.16932670X-RAY DIFFRACTION100
2.1933-2.28110.18961420.17262671X-RAY DIFFRACTION100
2.2811-2.38490.2641390.17742670X-RAY DIFFRACTION100
2.3849-2.51050.2131410.18432663X-RAY DIFFRACTION100
2.5105-2.66770.2351400.18532652X-RAY DIFFRACTION100
2.6677-2.87350.24151380.18742686X-RAY DIFFRACTION100
2.8735-3.16240.23411330.20042656X-RAY DIFFRACTION100
3.1624-3.61930.22781370.19832692X-RAY DIFFRACTION100
3.6193-4.55730.27431440.21442674X-RAY DIFFRACTION100
4.5573-29.49880.23071460.22412651X-RAY DIFFRACTION100

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