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- PDB-8w8v: High-resolution X-ray structure of cellulase Cel6A from Phaneroch... -

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Basic information

Entry
Database: PDB / ID: 8w8v
TitleHigh-resolution X-ray structure of cellulase Cel6A from Phanerochaete chrysosporium at cryogenic temperature, Enzyme-Product complex
ComponentsGlucanase
KeywordsHYDROLASE / Cellulase / Glycoside hydrolase family 6 / Cellobiohydrolase II
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region
Similarity search - Function
Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain ...Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain
Similarity search - Domain/homology
beta-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Glucanase
Similarity search - Component
Biological speciesPhanerodontia chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsTachioka, M. / Yamaguchi, S. / Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Yano, N. / Chatake, T. / Tamada, T. / Takeda, K. ...Tachioka, M. / Yamaguchi, S. / Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Yano, N. / Chatake, T. / Tamada, T. / Takeda, K. / Niwa, S. / Tanaka, H. / Takahashi, S. / Inaka, K. / Furubayashi, N. / Deguchi, S. / Samejima, M. / Igarashi, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H05494 Japan
Japan Society for the Promotion of Science (JSPS)23H00341, 19H03013, 18J01906, 15J10657 Japan
CitationJournal: To Be Published
Title: Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase
Authors: Tachioka, M. / Yamaguchi, S. / Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Yano, N. / Chatake, T. / Tamada, T. / Takeda, K. / Niwa, S. / Tanaka, H. / Takahashi, S. / Inaka, K. / ...Authors: Tachioka, M. / Yamaguchi, S. / Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Yano, N. / Chatake, T. / Tamada, T. / Takeda, K. / Niwa, S. / Tanaka, H. / Takahashi, S. / Inaka, K. / Furubayashi, N. / Deguchi, S. / Samejima, M. / Igarashi, K.
History
DepositionSep 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5499
Polymers38,3821
Non-polymers1,1688
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.044, 67.581, 88.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucanase


Mass: 38381.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerodontia chrysosporium (fungus) / Gene: cel6A / Production host: Komagataella pastoris (fungus) / References: UniProt: H3K419

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(4-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb4-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 551 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 293 K / Method: counter-diffusion
Details: polyethylene glycol 3350, sodium chloride, cellotriose, acetate buffer,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.85→100 Å / Num. obs: 547722 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.17
Reflection shellResolution: 0.85→0.9 Å / Rmerge(I) obs: 0.733 / Num. unique obs: 82938

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Processing

Software
NameClassification
SHELXLrefinement
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.85→46.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1186 --
Rwork0.1054 --
obs-282005 98.86 %
Refinement stepCycle: LAST / Resolution: 0.85→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 65 545 3320
LS refinement shellResolution: 0.85→0.88 Å
RfactorNum. reflection% reflection
Rfree0.2635 --
Rwork0.2541 --
obs-25374 89.71 %

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