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- PDB-6rzp: Multicrystal structure of Proteinase K at room temperature using ... -

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Basic information

Entry
Database: PDB / ID: 6rzp
TitleMulticrystal structure of Proteinase K at room temperature using a multilayer monochromator.
ComponentsProteinase K
KeywordsHYDROLASE / DMM / multilayer monochromator / multicrystal
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
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSandy, J. / Sandy, E. / Sanchez-Weatherby, J. / Mikolajek, H.
CitationJournal: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature crystallography at VMXi
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.G. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)29,3427
Polymers28,9591
Non-polymers3836
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-54 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.368, 68.368, 103.978
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-489-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 177 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.141.37
4
3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop7.51.2M Ammonium Sulfate, 0.1M Na Cacodylate pH 6.2, 25 % Glycerol
2934vapor diffusion, sitting drop7.51.2M Ammonium Sulfate, 0.1M Na Cacodylate pH 6.2, 25 % Glycerol
2933vapor diffusion, sitting drop7.51.2M Ammonium Sulfate, 0.1M Na Cacodylate pH 6.2, 25 % Glycerol
2932vapor diffusion, sitting drop7.51.2M Ammonium Sulfate, 0.1M Na Cacodylate pH 6.2, 25 % Glycerol

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Feb 1, 2019 / Details: multilayer monochromator
RadiationMonochromator: multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→57.13 Å / Num. obs: 13162 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 9.989 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.017 / Rrim(I) all: 0.066 / Net I/σ(I): 30.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 12.2 / Num. unique obs: 631 / CC1/2: 0.986 / Rpim(I) all: 0.052 / Rrim(I) all: 0.143 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ID8

2id8


Resolution: 2.2→57.126 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.55
RfactorNum. reflection% reflection
Rfree0.1611 1312 10.01 %
Rwork0.1055 --
obs0.111 13109 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→57.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 19 171 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092122
X-RAY DIFFRACTIONf_angle_d0.8952890
X-RAY DIFFRACTIONf_dihedral_angle_d2.8211633
X-RAY DIFFRACTIONf_chiral_restr0.052318
X-RAY DIFFRACTIONf_plane_restr0.006379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1996-2.28770.15581430.08971287X-RAY DIFFRACTION100
2.2877-2.39180.17041400.09461262X-RAY DIFFRACTION100
2.3918-2.51790.16931430.10071283X-RAY DIFFRACTION100
2.5179-2.67560.18041440.10451296X-RAY DIFFRACTION100
2.6756-2.88220.17481440.10191289X-RAY DIFFRACTION100
2.8822-3.17220.17361430.10761294X-RAY DIFFRACTION100
3.1722-3.63120.14811470.10181319X-RAY DIFFRACTION100
3.6312-4.57460.13261480.09441338X-RAY DIFFRACTION100
4.5746-57.14480.17261600.13651429X-RAY DIFFRACTION100

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