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- PDB-8x05: X-Ray crystal structure of glycoside hydrolase family 6 cellobioh... -

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Basic information

Entry
Database: PDB / ID: 8x05
TitleX-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/C393S soaked in cellotriose
ComponentsGlucanase
KeywordsHYDROLASE / Glycoside hydrolase family 6 / cellobiohydrolase / cellulase / catalytic domain / mutant
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
alpha-cellobiose / beta-D-glucopyranose / Glucanase
Similarity search - Component
Biological speciesPhanerodontia chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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: To Be Published
Title: Activity and X-ray crystal structure of candidate base catalyst mutants of glycoside hydrolase family 6 cellobiohydrolase
Authors: Yamaguchi, S. / Sunagawa, N. / Tachioka, M. / Igarashi, K.
History
DepositionNov 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: 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)38,8723
Polymers38,3491
Non-polymers5222
Water5,711317
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)54.150, 67.296, 85.926
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: 38349.445 Da / Num. of mol.: 1 / Mutation: C240S, C393S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerodontia chrysosporium (fungus) / Strain: K-3 / Gene: cel6A / Plasmid: pPICZalpha / 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: Polysaccharide beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / 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: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→45.81 Å / Num. obs: 117982 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 13.48 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 31.2
Reflection shellResolution: 1.13→1.15 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5784 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→45.81 Å / SU ML: 0.1352 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1532
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2067 2000 1.7 %
Rwork0.1905 115895 -
obs0.1908 117895 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.51 Å2
Refinement stepCycle: LAST / Resolution: 1.13→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 35 317 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543353
X-RAY DIFFRACTIONf_angle_d0.91274637
X-RAY DIFFRACTIONf_chiral_restr0.082511
X-RAY DIFFRACTIONf_plane_restr0.0069628
X-RAY DIFFRACTIONf_dihedral_angle_d5.7786472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.31031400.30028156X-RAY DIFFRACTION99.9
1.16-1.190.2991410.28428178X-RAY DIFFRACTION99.99
1.19-1.220.30061430.27338229X-RAY DIFFRACTION100
1.22-1.260.26821410.25768181X-RAY DIFFRACTION100
1.26-1.310.32181410.24478210X-RAY DIFFRACTION100
1.31-1.360.23351420.23428201X-RAY DIFFRACTION100
1.36-1.420.26261420.22968259X-RAY DIFFRACTION100
1.42-1.50.25291430.21888219X-RAY DIFFRACTION100
1.5-1.590.25531420.2068263X-RAY DIFFRACTION100
1.59-1.720.20871430.28265X-RAY DIFFRACTION99.99
1.72-1.890.21661430.20118279X-RAY DIFFRACTION100
1.89-2.160.19011440.18718376X-RAY DIFFRACTION100
2.16-2.720.19111450.18038384X-RAY DIFFRACTION99.99
2.72-45.810.1711500.15678695X-RAY DIFFRACTION100

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