[English] 日本語
Yorodumi
- PDB-4im4: Multifunctional cellulase, xylanase, mannanase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4im4
TitleMultifunctional cellulase, xylanase, mannanase
ComponentsEndoglucanase E
KeywordsHYDROLASE / cellulase / xylanase / mannanase / multifunction / Endo-1 / 4-beta-glucanase / biomass degradation
Function / homology
Function and homology information


glucomannan catabolic process / acetylxylan esterase / acetylxylan esterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / cellulose binding / cellulase / cellulase activity / xylan catabolic process / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate esterase 2, N-terminal / Carbohydrate esterase 2 N-terminal / CtCE2-like domain / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / Clostridium cellulosome enzymes repeated domain signature. / SGNH hydrolase superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain ...Carbohydrate esterase 2, N-terminal / Carbohydrate esterase 2 N-terminal / CtCE2-like domain / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / Clostridium cellulosome enzymes repeated domain signature. / SGNH hydrolase superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Cellulase/esterase CelE
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 Å
AuthorsBianchetti, C.M. / Takasuka, T.E. / Fox, B.G.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis.
Authors: Glasgow, E.M. / Kemna, E.I. / Bingman, C.A. / Ing, N. / Deng, K. / Bianchetti, C.M. / Takasuka, T.E. / Northen, T.R. / Fox, B.G.
History
DepositionJan 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / pdbx_database_related / Item: _citation.title
Revision 1.3Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Sep 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoglucanase E
B: Endoglucanase E
C: Endoglucanase E
D: Endoglucanase E
E: Endoglucanase E
F: Endoglucanase E


Theoretical massNumber of molelcules
Total (without water)229,1156
Polymers229,1156
Non-polymers00
Water23,6361312
1
A: Endoglucanase E


Theoretical massNumber of molelcules
Total (without water)38,1861
Polymers38,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase E


Theoretical massNumber of molelcules
Total (without water)38,1861
Polymers38,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endoglucanase E


Theoretical massNumber of molelcules
Total (without water)38,1861
Polymers38,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endoglucanase E


Theoretical massNumber of molelcules
Total (without water)38,1861
Polymers38,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Endoglucanase E


Theoretical massNumber of molelcules
Total (without water)38,1861
Polymers38,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Endoglucanase E


Theoretical massNumber of molelcules
Total (without water)38,1861
Polymers38,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.407, 111.701, 120.368
Angle α, β, γ (deg.)90.000, 97.290, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Endoglucanase E / Cellulase E / Endo-1 / 4-beta-glucanase E / EgE


Mass: 38185.832 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: celE / Plasmid: PVP67K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10477, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1312 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, 0.010 M MOPS pH 7.0) mixed in a 1:1 ratio with the Well Solution (9% PEG 20,000, 18% mmPEG 550,0.3 M diethyleneglycol, 0.3 M ...Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, 0.010 M MOPS pH 7.0) mixed in a 1:1 ratio with the Well Solution (9% PEG 20,000, 18% mmPEG 550,0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 M pentaethyleneglycol, 100mM MES/Imidazole buffer pH 6.5). Cryoprotected with 9% PEG 20,000, 18% mmPEG 550, 0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 M pentaethyleneglycol, 100mM MES/Imidazole buffer pH 6.5, 15% ethylene glycol, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2012 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 92255 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.193 / Χ2: 0.92 / Net I/σ(I): 3.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.42-2.463.40.62945110.782198
2.46-2.513.50.60545550.797198.3
2.51-2.553.70.55845310.804199
2.55-2.614.10.51745790.806199.7
2.61-2.664.20.51246110.814199.8
2.66-2.734.20.44346280.829199.8
2.73-2.794.20.41746180.839199.8
2.79-2.874.20.37445880.898199.7
2.87-2.954.20.31345830.925199.7
2.95-3.054.20.28846000.947199.8
3.05-3.164.20.25246280.982199.7
3.16-3.284.20.21546261.045199.8
3.28-3.434.20.19346151.108199.9
3.43-3.614.30.16246041.056199.8
3.61-3.844.30.1346551.0521100
3.84-4.144.30.11546151.023199.9
4.14-4.554.30.10346341.037199.9
4.55-5.214.30.09646541.0121100
5.21-6.564.30.10146890.9041100
6.56-504.10.07847310.631199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å47.35 Å
Translation2.5 Å47.35 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NDY

3ndy


Resolution: 2.42→47.352 Å / Occupancy max: 1 / Occupancy min: 0.13 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1994 2.16 %
Rwork0.2091 --
obs0.2103 92173 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.2 Å2 / Biso mean: 14.6576 Å2 / Biso min: 1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.42→47.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16164 0 0 1312 17476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916625
X-RAY DIFFRACTIONf_angle_d1.14622658
X-RAY DIFFRACTIONf_chiral_restr0.0772436
X-RAY DIFFRACTIONf_plane_restr0.0062945
X-RAY DIFFRACTIONf_dihedral_angle_d13.3435986
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.47940.32521400.23566246638697
2.4794-2.54650.31111390.22186370650999
2.5465-2.62140.28171420.217664236565100
2.6214-2.7060.28491430.227764256568100
2.706-2.80270.29641420.225164606602100
2.8027-2.91490.29161420.222564336575100
2.9149-3.04760.31781430.225664216564100
3.0476-3.20820.25951420.215864326574100
3.2082-3.40910.29261430.213664666609100
3.4091-3.67230.26511430.200464656608100
3.6723-4.04170.22831430.186464866629100
4.0417-4.62610.19831430.184365036646100
4.6261-5.82670.22611430.196365016644100
5.8267-47.36150.27111460.21846548669499

+
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