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- PDB-8x00: X-Ray crystal structure of glycoside hydrolase family 6 cellobioh... -

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Basic information

Entry
Database: PDB / ID: 8x00
TitleX-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/C393S/D394C
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: 1.53 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 2, 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)38,8102
Polymers38,3861
Non-polymers4241
Water8,017445
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)54.690, 67.490, 88.000
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: 38385.500 Da / Num. of mol.: 1 / Mutation: C240S, C393S, D394C
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
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 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→46.45 Å / Num. obs: 49937 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 19.19 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.3
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.553 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2425 / % possible all: 100

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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: 1.53→46.45 Å / SU ML: 0.1631 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1961 2000 4.01 %
Rwork0.1663 47858 -
obs0.1674 49872 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.52 Å2
Refinement stepCycle: LAST / Resolution: 1.53→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2711 0 28 445 3184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643077
X-RAY DIFFRACTIONf_angle_d0.84064265
X-RAY DIFFRACTIONf_chiral_restr0.0548474
X-RAY DIFFRACTIONf_plane_restr0.0064574
X-RAY DIFFRACTIONf_dihedral_angle_d5.7066446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.2931410.26043378X-RAY DIFFRACTION100
1.57-1.610.28031420.23893383X-RAY DIFFRACTION99.97
1.61-1.660.24811390.22033343X-RAY DIFFRACTION99.97
1.66-1.710.25611420.20553385X-RAY DIFFRACTION99.92
1.71-1.770.24531420.20163401X-RAY DIFFRACTION100
1.77-1.840.24021400.18753349X-RAY DIFFRACTION99.97
1.84-1.930.23861430.19253407X-RAY DIFFRACTION100
1.93-2.030.20221410.17383402X-RAY DIFFRACTION100
2.03-2.160.24671420.17653392X-RAY DIFFRACTION100
2.16-2.320.20991430.16553407X-RAY DIFFRACTION99.92
2.32-2.560.21091440.16823438X-RAY DIFFRACTION99.97
2.56-2.930.19251430.16873451X-RAY DIFFRACTION99.94
2.93-3.690.17211450.15323484X-RAY DIFFRACTION99.94
3.69-46.450.15691530.13823638X-RAY DIFFRACTION99.92

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