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- PDB-8xil: Cellodextrin phosphorylase from Clostridium thermocellum mutant -... -

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Basic information

Entry
Database: PDB / ID: 8xil
TitleCellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines
ComponentsCellodextrin phosphorylase
KeywordsCARBOHYDRATE / Cellulose / Cellodextrin / Synthesis / Phosphorolysis
Function / homology
Function and homology information


glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolase 94 / Glycosyl hydrolase 94, supersandwich domain / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
beta-cellotriose / ACETATE ION / DI(HYDROXYETHYL)ETHER / Cellodextrin phosphorylase
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsKuga, T. / Sunagawa, N. / Igarashi, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J12566 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H05494 Japan
CitationJournal: J Appl Glycosci (1999) / Year: 2024
Title: Effect of Free Cysteine Residues to Serine Mutation on Cellodextrin Phosphorylase.
Authors: Kuga, T. / Sunagawa, N. / Igarashi, K.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 25, 2024ID: 8H2W
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellodextrin phosphorylase
B: Cellodextrin phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,22450
Polymers225,3582
Non-polymers4,86648
Water37,8132099
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23290 Å2
ΔGint-73 kcal/mol
Surface area66930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.208, 88.778, 88.761
Angle α, β, γ (deg.)98.576, 110.545, 110.564
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Cellodextrin phosphorylase


Mass: 112679.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Strain: YM4 / Gene: cdp-ym4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93HT8
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 2145 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2099 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10 mg/ml protein solution was mixed 1:1 with an optimized solution consisting of 100 mM pH 5.0 sodium acetate, 12% PEG4000, and 5% glycerol with streak seeding

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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 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→43.82 Å / Num. obs: 611147 / % possible obs: 94.35 % / Redundancy: 7 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 1 / Net I/σ(I): 23.95
Reflection shellResolution: 1.21→1.253 Å / Mean I/σ(I) obs: 1.39 / Num. unique obs: 58904 / CC1/2: 0.736

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Processing

Software
NameVersionClassification
PHENIX1.21rc-5127refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→43.82 Å / SU ML: 0.1628 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.9237
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1635 30525 5.01 %
Rwork0.1427 578926 -
obs0.1437 609451 94.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.31 Å2
Refinement stepCycle: LAST / Resolution: 1.21→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15746 0 312 2099 18157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007217539
X-RAY DIFFRACTIONf_angle_d1.006823839
X-RAY DIFFRACTIONf_chiral_restr0.07922566
X-RAY DIFFRACTIONf_plane_restr0.00963135
X-RAY DIFFRACTIONf_dihedral_angle_d15.16796539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.430110070.427618019X-RAY DIFFRACTION88.36
1.22-1.240.39679930.386318362X-RAY DIFFRACTION90.04
1.24-1.250.33479850.310218648X-RAY DIFFRACTION91.27
1.25-1.270.29810640.276518616X-RAY DIFFRACTION91.36
1.27-1.290.29669220.261218821X-RAY DIFFRACTION91.53
1.29-1.30.33559970.313518577X-RAY DIFFRACTION90.83
1.3-1.320.27579900.254118922X-RAY DIFFRACTION92.36
1.32-1.340.331510200.317818903X-RAY DIFFRACTION92.74
1.34-1.360.295710330.263819006X-RAY DIFFRACTION92.9
1.36-1.390.24919500.209219116X-RAY DIFFRACTION93.14
1.39-1.410.207110090.166319114X-RAY DIFFRACTION93.35
1.41-1.430.187610080.151619036X-RAY DIFFRACTION93.52
1.43-1.460.170710870.137319092X-RAY DIFFRACTION93.7
1.46-1.490.16989260.133519240X-RAY DIFFRACTION93.76
1.49-1.520.161810340.124819323X-RAY DIFFRACTION94.35
1.52-1.560.15759930.129419392X-RAY DIFFRACTION94.67
1.56-1.60.15649930.130119370X-RAY DIFFRACTION94.83
1.6-1.640.158110290.126319486X-RAY DIFFRACTION95.11
1.64-1.690.14429880.115319524X-RAY DIFFRACTION95.4
1.69-1.750.154510580.120719610X-RAY DIFFRACTION95.64
1.75-1.810.143210450.11919593X-RAY DIFFRACTION95.94
1.81-1.880.151610650.123319684X-RAY DIFFRACTION96.15
1.88-1.970.16279530.142319520X-RAY DIFFRACTION95.34
1.97-2.070.143310280.126119813X-RAY DIFFRACTION96.79
2.07-2.20.136910880.123419767X-RAY DIFFRACTION97.09
2.2-2.370.147410790.130619804X-RAY DIFFRACTION96.76
2.37-2.610.142710730.124219993X-RAY DIFFRACTION97.73
2.61-2.980.14259940.129320153X-RAY DIFFRACTION98.14
2.98-3.760.148910310.128720155X-RAY DIFFRACTION98.45
3.76-43.820.146710830.134920267X-RAY DIFFRACTION99.24

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