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- PDB-9oyy: MicroED structure of proteinase K from microcrystals frozen by tr... -

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Basic information

Entry
Database: PDB / ID: 9oyy
TitleMicroED structure of proteinase K from microcrystals frozen by traditional cryoEM methods
ComponentsProteinase K
KeywordsHYDROLASE / enzyme / MicroED
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / 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. ...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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.2 Å
AuthorsVlahakis, N. / Summers, J.A. / Rodriguez, J.A. / Dahlberg, P. / Wakatsuki, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Mix-and-spray grid preparation for time-resolved MicroED
Authors: Summers, J.A. / Vlahakis, N.W. / Zielinski, K.A. / Uttormark, S. / Dolamore, C. / Antolini, C. / Wilson, M.A. / Pollack, L. / Rodriguez, J.A. / Dahlberg, P.D. / Wakatsuki, S.
History
DepositionJun 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
B: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0786
Polymers57,9182
Non-polymers1604
Water32418
1
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0393
Polymers28,9591
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0393
Polymers28,9591
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.300, 129.100, 47.700
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proteinase K / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.791 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Proteinase K / Type: COMPLEX
Details: Crystals formed from 50 mg/mL proteinase K mixed 1:1 with reservoir solution (0.1 M Tris HCl pH 8.0, 1.2 M ammonium sulfate)
Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Parengyodontium album (fungus)
EM crystal formationDetails: Crystals formed from 50 mg/mL proteinase K mixed 1:1 with reservoir solution (0.1 M Tris HCl pH 8.0, 1.2 M ammonium sulfate)
Temperature: 293 K
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm
Specimen holderTemperature (max): 100 K / Temperature (min): 100 K
Image recordingElectron dose: 0.15 e/Å2 / Film or detector model: FEI CETA (4k x 4k)
EM diffraction shellResolution: 2.2→2.3 Å / Fourier space coverage: 59.55 % / Multiplicity: 3.29 / Num. of structure factors: 1409 / Phase residual: 33.9 °
EM diffraction statsFourier space coverage: 79.86 % / High resolution: 2.2 Å / Num. of intensities measured: 120010 / Num. of structure factors: 36443 / Phase error rejection criteria: not provided / Rmerge: 0.266

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Processing

EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 38.3 Å / B: 129.1 Å / C: 47.7 Å / Space group name: P21 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution: 2.2 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingPDB-ID: 2ID8

2id8


Accession code: 2ID8 / Source name: PDB / Type: experimental model
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.94 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.33 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23713 918 5.1 %RANDOM
Rwork0.21002 ---
obs0.21143 16982 76.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.078 Å2
Baniso -1Baniso -2Baniso -3
1--20.94 Å2-0 Å21.84 Å2
2--34.72 Å20 Å2
3----13.78 Å2
Refinement stepCycle: 1 / Total: 4092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0080.0124148
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0010.0163703
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.6671.775636
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.6031.7258535
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg6.3945556
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg5.578522
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg13.97610605
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_4_deg
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0770.2623
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0070.025078
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0010.02982
ELECTRON CRYSTALLOGRAPHYr_nbd_refined
ELECTRON CRYSTALLOGRAPHYr_nbd_other
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined
ELECTRON CRYSTALLOGRAPHYr_nbtor_other
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_other
ELECTRON CRYSTALLOGRAPHYr_metal_ion_refined
ELECTRON CRYSTALLOGRAPHYr_metal_ion_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_vdw_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_vdw_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_hbond_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_hbond_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_metal_ion_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_metal_ion_other
ELECTRON CRYSTALLOGRAPHYr_mcbond_it4.5112.1762230
ELECTRON CRYSTALLOGRAPHYr_mcbond_other4.4832.1772230
ELECTRON CRYSTALLOGRAPHYr_mcangle_it6.0083.9112784
ELECTRON CRYSTALLOGRAPHYr_mcangle_other6.0093.9132785
ELECTRON CRYSTALLOGRAPHYr_scbond_it6.7732.8661918
ELECTRON CRYSTALLOGRAPHYr_scbond_other6.7712.8681919
ELECTRON CRYSTALLOGRAPHYr_scangle_it
ELECTRON CRYSTALLOGRAPHYr_scangle_other9.8874.9582853
ELECTRON CRYSTALLOGRAPHYr_long_range_B_refined11.13235.9617722
ELECTRON CRYSTALLOGRAPHYr_long_range_B_other11.13235.9717723
ELECTRON CRYSTALLOGRAPHYr_rigid_bond_restr
ELECTRON CRYSTALLOGRAPHYr_sphericity_free
ELECTRON CRYSTALLOGRAPHYr_sphericity_bonded
LS refinement shellResolution: 2.2→2.457 Å
RfactorNum. reflection% reflection
Rfree0.294 234 -
Rwork0.237 4268 -
obs--67.69 %

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