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- PDB-4im4: Multifunctional cellulase, xylanase, mannanase -

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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. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / SGNH hydrolase superfamily ...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. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / SGNH hydrolase superfamily / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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