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- PDB-5i9s: MicroED structure of proteinase K at 1.75 A resolution -

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Basic information

Entry
Database: PDB / ID: 5i9s
TitleMicroED structure of proteinase K at 1.75 A resolution
ComponentsProteinase K
KeywordsHYDROLASE
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/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. ...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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEngyodontium album (fungus)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.75 Å
AuthorsHattne, J. / Shi, D. / de la Cruz, M.J. / Reyes, F.E. / Gonen, T.
CitationJournal: J Appl Crystallogr / Year: 2016
Title: Modeling truncated pixel values of faint reflections in MicroED images.
Authors: Johan Hattne / Dan Shi / M Jason de la Cruz / Francis E Reyes / Tamir Gonen /
Abstract: The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated ...The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected micro-electron diffraction (MicroED) images.
History
DepositionFeb 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Other
Revision 1.3Nov 30, 2016Group: Refinement description
Revision 1.4Jul 18, 2018Group: Data collection / Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.5Aug 22, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.6Aug 30, 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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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1513
Polymers28,9591
Non-polymers1922
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-27 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.317, 67.317, 101.007
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-480-

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) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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 / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.02898 MDa / Experimental value: NO
Source (natural)Organism: Engyodontium album (fungus)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
11.2 Mammonium sulfate1
20.1 MTris1
SpecimenConc.: 25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 0.004 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 184 / Num. of grids imaged: 1 / Num. of real images: 184
Image scansSampling size: 0.0311999992 µm / Width: 2048 / Height: 2048
EM diffractionCamera length: 1200 mm
EM diffraction shellResolution: 1.75→1.8065 Å / Fourier space coverage: 94 % / Multiplicity: 4.4 / Num. of structure factors: 2006 / Phase residual: 56.6 °
EM diffraction statsFourier space coverage: 69 % / High resolution: 1.3 Å / Num. of intensities measured: 154259 / Num. of structure factors: 39563 / Phase error: 28.86 ° / Phase residual: 37.73 ° / Phase error rejection criteria: 0 / Rmerge: 62.9 / Rsym: 62.9

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Processing

SoftwareName: PHENIX / Version: (1.10_2155: ???) / Classification: refinement
EM software
IDNameVersionCategory
1EM-Menu4.0.9.75image acquisition
6MOLREP11.4.03model fitting
8MOLREP11.4.03molecular replacement
11POINTLESS1.10.13symmetry determination
12AIMLESS0.5.17crystallography merging
14PHENIX1.1model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 67.96 Å / B: 67.96 Å / C: 101.73 Å / Space group name: P43212 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 1.75 Å / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 17.2 / Protocol: OTHER / Space: RECIPROCAL / Details: Electron scattering factors
Atomic model buildingPDB-ID: 4WOC

4woc


Pdb chain-ID: A / Pdb chain residue range: 1-279
RefinementResolution: 1.75→20.506 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1476 6.51 %RANDOM
Rwork0.2167 ---
obs0.2199 22671 94.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0032076
ELECTRON CRYSTALLOGRAPHYf_angle_d0.5652824
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d9.281212
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.041312
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.003370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.41791360.34751870ELECTRON CRYSTALLOGRAPHY94
1.8065-1.8710.40441300.31261921ELECTRON CRYSTALLOGRAPHY95
1.871-1.94590.32381390.28041875ELECTRON CRYSTALLOGRAPHY95
1.9459-2.03430.32141350.25831932ELECTRON CRYSTALLOGRAPHY95
2.0343-2.14150.32541270.24351900ELECTRON CRYSTALLOGRAPHY95
2.1415-2.27550.26841360.22841903ELECTRON CRYSTALLOGRAPHY94
2.2755-2.45090.31281350.22551918ELECTRON CRYSTALLOGRAPHY94
2.4509-2.69710.26691350.22511936ELECTRON CRYSTALLOGRAPHY94
2.6971-3.08620.2511320.2071939ELECTRON CRYSTALLOGRAPHY94
3.0862-3.8840.1821300.16181958ELECTRON CRYSTALLOGRAPHY94
3.884-20.50760.19651410.15712043ELECTRON CRYSTALLOGRAPHY92

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