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- PDB-8wwt: X-Ray crystal structure of glycoside hydrolase family 6 cellobioh... -

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Basic information

Entry
Database: PDB / ID: 8wwt
TitleX-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C393S
ComponentsGlucanase
KeywordsHYDROLASE / Glycoside hydrolase family 6 / cellobiohydrolase / cellulase / catalytic domain / free cysteine
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
Biological speciesPhanerodontia chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsYamaguchi, S. / Sunagawa, N. / Tachioka, M. / Igarashi, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J12651 Japan
CitationJournal: J Appl Glycosci (1999) / Year: 2024
Title: Thermotolerance Mechanism of Fungal GH6 Cellobiohydrolase. Part II. Structural Analysis of Thermotolerant Mutant from the Basidiomycete Phanerochaete chrysosporium.
Authors: Yamaguchi, S. / Sunagawa, N. / Samejima, M. / Igarashi, K.
History
DepositionOct 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucanase


Theoretical massNumber of molelcules
Total (without water)38,3661
Polymers38,3661
Non-polymers00
Water9,098505
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Software (PISA) determined protein interfaces have not revealed any specific interactions that could form stable quaternary structures.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.498, 67.367, 88.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glucanase


Mass: 38365.512 Da / Num. of mol.: 1 / Mutation: C393S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerodontia chrysosporium (fungus) / Strain: K-3 / Gene: cel6A / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H
References: UniProt: H3K419, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 4000, sodium acetate, sodium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→46.39 Å / Num. obs: 175525 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 9.67 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 33.1
Reflection shellResolution: 1→1.02 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.037 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8575 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→46.39 Å / SU ML: 0.0719 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.2486
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1691 2000 1.14 %
Rwork0.1532 173416 -
obs0.1534 175416 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.74 Å2
Refinement stepCycle: LAST / Resolution: 1→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 0 505 3215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484098
X-RAY DIFFRACTIONf_angle_d0.84915677
X-RAY DIFFRACTIONf_chiral_restr0.0794621
X-RAY DIFFRACTIONf_plane_restr0.0076775
X-RAY DIFFRACTIONf_dihedral_angle_d5.5184591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.030.23881410.228112223X-RAY DIFFRACTION99.37
1.03-1.050.21891410.205512233X-RAY DIFFRACTION99.85
1.05-1.080.19261420.182112284X-RAY DIFFRACTION99.98
1.08-1.120.18221420.166812300X-RAY DIFFRACTION100
1.12-1.160.16691410.158612288X-RAY DIFFRACTION99.98
1.16-1.210.15441420.151512308X-RAY DIFFRACTION100
1.21-1.260.15351420.151812302X-RAY DIFFRACTION99.98
1.26-1.330.16121430.151712336X-RAY DIFFRACTION99.99
1.33-1.410.15821430.15212374X-RAY DIFFRACTION100
1.41-1.520.15681420.144712392X-RAY DIFFRACTION100
1.52-1.670.17551430.145512424X-RAY DIFFRACTION100
1.67-1.910.14791430.149412451X-RAY DIFFRACTION99.98
1.91-2.410.16811460.152512565X-RAY DIFFRACTION99.99
2.41-46.390.17411490.147212936X-RAY DIFFRACTION99.98

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