[English] 日本語
Yorodumi
- EMDB-8218: MicroED structure of xylanase at 2.3 A resolution -

+
Open data


ID or keywords:

Loading...

-
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 activity / endo-1,4-beta-xylanase / 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

-
Structure visualization

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

emd_8218.png

Downloads & links

-
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

-
Supplemental data

-
Sample components

-
Entire : Xylanase

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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

-
Sample preparation

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

-
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

+
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more