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- PDB-7c0p: Structure of proteinase K obtained in SSRF using serial crystallo... -

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Basic information

Entry
Database: PDB / ID: 7c0p
TitleStructure of proteinase K obtained in SSRF using serial crystallography
ComponentsProteinase K
KeywordsHYDROLASE
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. / Peptidase S8, subtilisin, Ser-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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhao, F.Z.
CitationJournal: Lab Chip / Year: 2020
Title: A novel sample delivery system based on circular motion for in situ serial synchrotron crystallography.
Authors: Zhao, F.Z. / Sun, B. / Yu, L. / Xiao, Q.J. / Wang, Z.J. / Chen, L.L. / Liang, H. / Wang, Q.S. / He, J.H. / Yin, D.C.
History
DepositionMay 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,9992
Polymers28,9591
Non-polymers401
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-11 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.000, 69.000, 107.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-466-

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 natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 44.06 %
Crystal growTemperature: 293 K / Method: microbatch / Details: PEG 20000, Tris-HCl pH 8.5, Ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→31.684 Å / Num. obs: 14441 / % possible obs: 98.16 % / Redundancy: 8.39 % / R split: 0.2878 / Net I/σ(I): 5.06
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 1203 / R split: 0.6214

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FJS

6fjs


Resolution: 2.15→31.684 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.75
RfactorNum. reflection% reflection
Rfree0.2073 1438 9.99 %
Rwork0.1832 --
obs0.1857 14395 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.45 Å2 / Biso mean: 60.6727 Å2 / Biso min: 42.43 Å2
Refinement stepCycle: final / Resolution: 2.15→31.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 1 107 2139
Biso mean--57.17 69.1 -
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1501-2.22690.37181370.3033122695
2.2269-2.3160.26031380.2329125797
2.316-2.42140.27991370.2278125298
2.4214-2.5490.25861400.2252125997
2.549-2.70860.25491440.2165129098
2.7086-2.91760.28451420.2136128099
2.9176-3.2110.24691430.2066129299
3.211-3.6750.19361480.18391324100
3.675-4.62780.16541490.15421347100
4.6278-31.6840.19051600.1704143099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0243-0.06010.04520.80480.31051.10650.03740.1785-0.0052-0.32810.0336-0.1205-0.08350.0055-0.07860.6168-0.01310.01350.49670.01130.519316.175421.213521.614
21.80620.6648-0.31031.002-0.15180.79040.1014-0.21690.07770.1288-0.03060.0744-0.0766-0.0529-0.1280.5715-0.0010.01130.49360.00090.55756.446415.00430.7849
31.12260.29010.01421.05610.08940.8676-0.0075-0.0836-0.1587-0.07850.0388-0.05010.12230.0717-0.04460.50710.00110.02440.50660.01210.529814.59623.607130.3759
41.1249-0.64010.18840.70860.25940.85270.04730.00370.0233-0.17580.0206-0.1863-0.04830.0855-0.04470.5692-0.02750.04670.55950.01220.53824.89712.261525.6874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )A1 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 120 )A59 - 120
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 183 )A121 - 183
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 279 )A184 - 279

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