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- EMDB-8218: MicroED structure of xylanase at 2.3 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-8218
TitleMicroED structure of xylanase at 2.3 A resolution
Map dataXylanase
Sample
  • Organelle or cellular component: Xylanase
    • Protein or peptide: Endo-1,4-beta-xylanase 2
  • Ligand: IODIDE ION
  • Ligand: water
KeywordsHydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesTrichoderma reesei (fungus) / Hypocrea jecorina (fungus)
Methodelectron crystallography / cryo EM / Resolution: 2.3 Å
Authorsde la Cruz MJ / Hattne J
CitationJournal: Nat Methods / Year: 2017
Title: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.
Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen /
Abstract: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.
History
DepositionMay 26, 2016-
Header (metadata) releaseJun 22, 2016-
Map releaseJun 22, 2016-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5k7p
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5k7p
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8218.png

Downloads & links

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Map

FileDownload / File: emd_8218.map.gz / Format: CCP4 / Size: 1.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationXylanase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.79 Å/pix.
x 61 pix.
= 69.812 Å		0.75 Å/pix.
x 67 pix.
= 48.161 Å		0.75 Å/pix.
x 71 pix.
= 59.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.75252 Å / Y: 0.7469 Å / Z: 0.79332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.04 / Movie #1: 0.025
Minimum - Maximum-0.066510156 - 0.1118733
Average (Standard dev.)0.000108788234 (±0.018957304)
SymmetrySpace group: 19
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-48-41-8
Dimensions677161
Spacing648088
CellA: 48.1611 Å / B: 59.7521 Å / C: 69.812 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.7525156250.74690.79331818181818
M x/y/z648088
origin x/y/z0.0000.0000.000
length x/y/z48.16159.75269.812
α/β/γ90.00090.00090.000
start NX/NY/NZ-48-41-8
NX/NY/NZ677161
MAP C/R/S213
start NC/NR/NS-41-48-8
NC/NR/NS716761
D min/max/mean-0.0670.1120.000

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Supplemental data

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Sample components

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Entire : Xylanase

EntireName: Xylanase
Components
  • Organelle or cellular component: Xylanase
    • Protein or peptide: Endo-1,4-beta-xylanase 2
  • Ligand: IODIDE ION
  • Ligand: water

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Supramolecule #1: Xylanase

SupramoleculeName: Xylanase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Trichoderma reesei (fungus)
Molecular weightTheoretical: 21.035 KDa

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Macromolecule #1: Endo-1,4-beta-xylanase 2

MacromoleculeName: Endo-1,4-beta-xylanase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: endo-1,4-beta-xylanase
Source (natural)Organism: Hypocrea jecorina (fungus)
Molecular weightTheoretical: 20.855467 KDa
SequenceString:
QTIQPGTGYN NGYFYSYWND GHGGVTYTNG PGGQFSVNWS NSGNFVGGKG WQPGTKNKVI NFSGSYNPNG NSYLSVYGWS RNPLIEYYI VENFGTYNPS TGATKLGEVT SDGSVYDIYR TQRVNQPSII GTATFYQYWS VRRNHRSSGS VNTANHFNAW A QQGLTLGT MDYQIVAVEG YFSSGSASIT VS

UniProtKB: Endo-1,4-beta-xylanase 2

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Macromolecule #2: IODIDE ION

MacromoleculeName: IODIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: IOD
Molecular weightTheoretical: 126.904 Da
Chemical component information

ChemComp-IOD:
IODIDE ION

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 23 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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

BufferpH: 9
Component:
ConcentrationFormulaName
0.3 MNaIsodium iodide
1.25 MNH4SO4ammonium sulfate
100.0 mMbicine
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
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: 588 / Number diffraction images: 588 / Average exposure time: 4.1 sec. / Average electron dose: 0.004 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1750 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Molecular replacementSoftware - Name: MOLREP (ver. 11.4.05) / Software - details: Starting model PDB ID 2dfb
Symmetry determination software listSoftware - Name: POINTLESS (ver. 1.10.21)
Merging software listSoftware - Name: AIMLESS (ver. 0.5.25)
Crystallography statisticsNumber intensities measured: 38699 / Number structure factors: 10664 / Fourier space coverage: 66.6 / R sym: 0.428 / R merge: 0.428 / Overall phase error: 29.95 / Overall phase residual: 44.49 / Phase error rejection criteria: 0 / High resolution: 1.9 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.3 Å / Shell - Low resolution: 2.63 Å / Shell - Number structure factors: 2285 / Shell - Phase residual: 53.8 / Shell - Fourier space coverage: 74.9 / Shell - Multiplicity: 3.8

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Atomic model buiding 1

Initial modelPDB ID:

2dfb


Chain - Chain ID: A / Chain - Residue range: 1-190 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-5k7p:
MicroED structure of xylanase at 2.3 A resolution

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