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

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Basic information

Entry
Database: PDB / ID: 8wxc
TitleX-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A D170N/C240S/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: 0.95 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
DepositionOct 28, 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


Theoretical massNumber of molelcules
Total (without water)38,3481
Polymers38,3481
Non-polymers00
Water8,665481
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)54.534, 67.555, 88.673
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: 38348.461 Da / Num. of mol.: 1 / Mutation: D170N, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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: 0.95→46.45 Å / Num. obs: 202760 / % possible obs: 98.5 % / Redundancy: 11.9 % / Biso Wilson estimate: 9.06 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.6
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 7911 / % possible all: 78.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→46.45 Å / SU ML: 0.0671 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1763 1998 9.9 %
Rwork0.1651 200644 -
obs0.1652 202642 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.73 Å2
Refinement stepCycle: LAST / Resolution: 0.95→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 0 481 3191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493297
X-RAY DIFFRACTIONf_angle_d0.88964573
X-RAY DIFFRACTIONf_chiral_restr0.0839507
X-RAY DIFFRACTIONf_plane_restr0.0076618
X-RAY DIFFRACTIONf_dihedral_angle_d5.7286482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.970.2311180.233611769X-RAY DIFFRACTION81.37
0.97-10.21071390.207813993X-RAY DIFFRACTION97.32
1-1.030.20321440.189314399X-RAY DIFFRACTION99.86
1.03-1.060.18641430.1814429X-RAY DIFFRACTION100
1.06-1.10.15381450.166414462X-RAY DIFFRACTION99.99
1.1-1.140.16621430.162714484X-RAY DIFFRACTION99.99
1.14-1.20.16451440.161414440X-RAY DIFFRACTION99.99
1.2-1.260.18271450.162614466X-RAY DIFFRACTION99.99
1.26-1.340.1791430.162714551X-RAY DIFFRACTION99.99
1.34-1.440.16221460.16214552X-RAY DIFFRACTION100
1.44-1.590.17841450.156414564X-RAY DIFFRACTION100
1.59-1.820.16561460.16114644X-RAY DIFFRACTION99.99
1.82-2.290.14111470.167114727X-RAY DIFFRACTION100
2.29-46.450.20011500.160815164X-RAY DIFFRACTION99.98

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