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- EMDB-8077: MicroED structure of proteinase K at 1.75 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-8077
TitleMicroED structure of proteinase K at 1.75 A resolution
Map dataNone
Sample
  • Complex: Proteinase K
    • Protein or peptide: Proteinase K
  • Ligand: SULFATE IONSulfate
  • Ligand: water
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 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 speciesEngyodontium album (fungus)
Methodelectron crystallography / cryo EM / Resolution: 1.75 Å
AuthorsHattne J / Shi D
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
DepositionApr 14, 2016-
Header (metadata) releaseMay 4, 2016-
Map releaseJun 8, 2016-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5i9s
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5i9s
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8077.png

Downloads & links

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Map

FileDownload / File: emd_8077.map.gz / Format: CCP4 / Size: 3.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.57 Å/pix.
x 96 pix.
= 101.007 Å		0.6 Å/pix.
x 89 pix.
= 67.317 Å		0.6 Å/pix.
x 98 pix.
= 67.317 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.60105 Å / Y: 0.60105 Å / Z: 0.5739 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.15 / Movie #1: 0.25
Minimum - Maximum-0.46426287 - 1.267889
Average (Standard dev.)0.00013379476 (±0.16767947)
SymmetrySpace group: 96
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-25-77-48
Dimensions899896
Spacing112112176
CellA: 67.3174 Å / B: 67.3174 Å / C: 101.007 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.601044642857140.601044642857140.57390340909091
M x/y/z112112176
origin x/y/z0.0000.0000.000
length x/y/z67.31767.317101.007
α/β/γ90.00090.00090.000
start NX/NY/NZ-25-77-48
NX/NY/NZ899896
MAP C/R/S213
start NC/NR/NS-77-25-48
NC/NR/NS988996
D min/max/mean-0.4641.2680.000

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Supplemental data

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Sample components

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Entire : Proteinase K

EntireName: Proteinase K
Components
  • Complex: Proteinase K
    • Protein or peptide: Proteinase K
  • Ligand: SULFATE IONSulfate
  • Ligand: water

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Supramolecule #1: Proteinase K

SupramoleculeName: Proteinase K / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Engyodontium album (fungus)
Molecular weightTheoretical: 28.98 KDa

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Macromolecule #1: Proteinase K

MacromoleculeName: Proteinase K / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidase K
Source (natural)Organism: Engyodontium album (fungus)
Molecular weightTheoretical: 28.958791 KDa
SequenceString: AAQTNAPWGL ARISSTSPGT STYYYDESAG QGSCVYVIDT GIEASHPEFE GRAQMVKTYY YSSRDGNGHG THCAGTVGSR TYGVAKKTQ LFGVKVLDDN GSGQYSTIIA GMDFVASDKN NRNCPKGVVA SLSLGGGYSS SVNSAAARLQ SSGVMVAVAA G NNNADARN ...String:
AAQTNAPWGL ARISSTSPGT STYYYDESAG QGSCVYVIDT GIEASHPEFE GRAQMVKTYY YSSRDGNGHG THCAGTVGSR TYGVAKKTQ LFGVKVLDDN GSGQYSTIIA GMDFVASDKN NRNCPKGVVA SLSLGGGYSS SVNSAAARLQ SSGVMVAVAA G NNNADARN YSPASEPSVC TVGASDRYDR RSSFSNYGSV LDIFGPGTDI LSTWIGGSTR SISGTSMATP HVAGLAAYLM TL GKTTAAS ACRYIADTAN KGDLSNIPFG TVNLLAYNNY QA

UniProtKB: Proteinase K

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Macromolecule #2: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION / Sulfate

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 133 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

Concentration25 mg/mL
BufferpH: 8 / Component:
ConcentrationName
1.2 Mammonium sulfate
0.1 MTris
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1200 mm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 184 / Number diffraction images: 184 / Average exposure time: 4.1 sec. / Average electron dose: 0.004 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Crystallography statisticsNumber intensities measured: 154259 / Number structure factors: 39563 / Fourier space coverage: 69 / R sym: 62.9 / R merge: 62.9 / Overall phase error: 28.86 / Overall phase residual: 37.73 / Phase error rejection criteria: 0 / High resolution: 1.3 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.75 Å / Shell - Low resolution: 1.8065 Å / Shell - Number structure factors: 2006 / Shell - Phase residual: 56.6 / Shell - Fourier space coverage: 94 / Shell - Multiplicity: 4.4
Molecular replacementSoftware - Name: MOLREP (ver. 11.4.03)
Symmetry determination software listSoftware - Name: POINTLESS (ver. 1.10.13)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.75 Å
Merging software listSoftware - Name: AIMLESS (ver. 0.5.17)

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Atomic model buiding 1

Initial modelPDB ID:

4woc


Chain - Chain ID: A / Chain - Residue range: 1-279
DetailsElectron scattering factors
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 17.2
Output model

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

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