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- PDB-8x04: X-Ray crystal structure of glycoside hydrolase family 6 cellobioh... -

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Basic information

Entry
Database: PDB / ID: 8x04
TitleX-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/C393S/D394A
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
Biological speciesPhanerodontia chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 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

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Assembly

Deposited unit
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5272
Polymers38,3051
Non-polymers2211
Water9,584532
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)54.813, 67.825, 88.258
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: 38305.438 Da / Num. of mol.: 1 / Mutation: C240S, C393S, D394A
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
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / 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: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.97→46.56 Å / Num. obs: 190992 / % possible obs: 98.4 % / Redundancy: 12.1 % / Biso Wilson estimate: 10.17 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 37.1
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8866 / % possible all: 93.6

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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: 0.97→38.39 Å / SU ML: 0.0757 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.2991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1792 2000 1.05 %
Rwork0.1612 188896 -
obs0.1612 190896 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.27 Å2
Refinement stepCycle: LAST / Resolution: 0.97→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 14 532 3253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053911
X-RAY DIFFRACTIONf_angle_d0.88555421
X-RAY DIFFRACTIONf_chiral_restr0.0828603
X-RAY DIFFRACTIONf_plane_restr0.0067734
X-RAY DIFFRACTIONf_dihedral_angle_d5.738568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.990.25081340.218312687X-RAY DIFFRACTION93.42
0.99-1.020.19961370.19512881X-RAY DIFFRACTION94.83
1.02-1.050.17911380.182113098X-RAY DIFFRACTION96.05
1.05-1.090.16211390.164713181X-RAY DIFFRACTION97.02
1.09-1.120.15321420.156913334X-RAY DIFFRACTION97.69
1.12-1.170.16481420.152313473X-RAY DIFFRACTION98.66
1.17-1.220.14661440.154513538X-RAY DIFFRACTION99.3
1.22-1.290.16331440.152513567X-RAY DIFFRACTION99.33
1.29-1.370.18351440.159213685X-RAY DIFFRACTION99.68
1.37-1.470.16931460.156313687X-RAY DIFFRACTION99.87
1.47-1.620.17461450.152813736X-RAY DIFFRACTION99.96
1.62-1.860.19031470.161513838X-RAY DIFFRACTION99.99
1.86-2.340.17691470.166813890X-RAY DIFFRACTION99.97
2.34-38.390.18181510.158314301X-RAY DIFFRACTION99.94

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