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- PDB-7nuy: New polymorhp of proteinase K obtained by free interface diffusio... -

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Basic information

Entry
Database: PDB / ID: 7nuy
TitleNew polymorhp of proteinase K obtained by free interface diffusion technique
ComponentsProteinase K
KeywordsHYDROLASE / PROTEINASE K / SERINE PROTEASES
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: 1.65 Å
AuthorsGavira, J.A. / Artusio, F. / Castellvi, A. / Pisano, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2016-74875-P Spain
CitationJournal: Crystals / Year: 2021
Title: Tuning Transport Phenomena in Agarose Gels for the Control of Protein Nucleation Density and Crystal Form
Authors: Artusio, F. / Castellvi, A. / Pisano, R. / Gavira, J.A.
History
DepositionMar 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3435
Polymers28,9591
Non-polymers3844
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-36 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.500, 70.960, 78.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.71 Å3/Da / Density % sol: 28.3 % / Description: acicular
Crystal growTemperature: 293.5 K / Method: liquid diffusion / pH: 8
Details: Free interface diffusion: 1.8 M (NH4)2SO4, 0.1 M Tris pH 8.0
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→78.75 Å / Num. obs: 23985 / % possible obs: 90.2 % / Redundancy: 4 % / Biso Wilson estimate: 10.67 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.071 / Rrim(I) all: 0.144 / Net I/σ(I): 7.4 / Num. measured all: 95142 / Scaling rejects: 227
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.684.20.50410650.5530.2770.57981.6
9.04-78.7540.0441870.9950.0240.05194.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NUZ

7nuz


Resolution: 1.65→52.72 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 1156 4.83 %
Rwork0.1723 22765 -
obs0.1746 23921 89.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.38 Å2 / Biso mean: 12.9669 Å2 / Biso min: 4.6 Å2
Refinement stepCycle: final / Resolution: 1.65→52.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 20 428 2480
Biso mean--28.21 22.15 -
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.730.28021230.22082552267582
1.73-1.820.29181540.22052505265981
1.82-1.930.22841220.19992499262179
1.93-2.080.24861300.18222760289088
2.08-2.290.26321430.17013052319597
2.29-2.620.20051470.17213072321997
2.62-3.30.1981860.15743061324797
3.3-52.720.18461510.15353264341596
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)
10.79190.05550.37840.26180.06941.5336-0.03990.00420.0755-0.0319-0.0115-0.0044-0.1268-0.10860.05050.06330.01340.00340.05470.00890.068218.516.6071-10.0927
21.5065-0.23240.58280.5277-0.11031.8560.0459-0.07580.08930.031-0.0464-0.09110.02710.12320.0330.0519-0.0229-0.00140.0669-0.00470.08726.98694.1819-0.4043
34.0634-1.91042.07254.7092-3.24963.3051-0.1382-0.14580.03210.11930.1576-0.0091-0.05410.0508-0.05590.0805-0.00830.01390.084-0.030.066618.79241.934412.5041
40.4850.21390.00450.1194-0.09750.69370.0534-0.02620.0392-0.0613-0.0836-0.0227-0.02890.0850.02290.09030.0178-0.00490.1116-0.01520.074115.63060.81933.8789
50.8208-1.2191-0.92282.34261.26682.4169-0.0284-0.1191-0.00590.08180.1322-0.02440.05870.029-0.08510.0346-0.0197-0.00890.1026-0.00750.054915.3636-9.64685.5855
61.0144-0.1953-0.44571.0898-0.27143.9060.0359-0.03940.0021-0.0239-0.0222-0.02760.1813-0.10590.00180.0446-0.0082-0.00860.0509-0.00610.058816.3782-13.0576-6.2798
71.74912.08870.20254.64460.92870.5226-0.00540.03260.024-0.0956-0.0501-0.0774-0.0095-0.01830.0040.06930.0011-0.01470.07210.00880.0429.7316-0.4005-11.3254
81.189-0.7268-0.14091.70340.83410.996-0.0393-0.01380.0012-0.0348-0.02050.0657-0.0084-0.08920.06320.0562-0.0030.0010.07990.00750.03078.6746-3.6783-7.924
91.1287-0.5087-0.11056.747-3.2982.84260.09030.10660.02340.0060.00970.4705-0.0845-0.057-0.11570.0486-0.0044-0.01510.1136-0.010.06677.3065-7.8146-13.6055
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 103 )A59 - 103
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 120 )A104 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 138 )A121 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 168 )A139 - 168
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 204 )A169 - 204
7X-RAY DIFFRACTION7chain 'A' and (resid 205 through 222 )A205 - 222
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 264 )A223 - 264
9X-RAY DIFFRACTION9chain 'A' and (resid 265 through 279 )A265 - 279

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