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- PDB-5jx5: GH6 Orpinomyces sp. Y102 enzyme -

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Basic information

Entry
Database: PDB / ID: 5jx5
TitleGH6 Orpinomyces sp. Y102 enzyme
ComponentsGlucanase
KeywordsHYDROLASE / Orpinomyces sp. / GH6 / Cbh7 / endoglucanases / exoglucanases
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Fungal dockerin domain superfamily / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glucanase
Similarity search - Component
Biological speciesOrpinomyces sp. Y102 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsTsai, L.C. / Huang, H.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
NSCNSC101-2311-B-027-001 Taiwan
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2019
Title: Crystal structures of GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo- and endo- activity in a complex with cellobiose
Authors: Huang, H.C. / Qi, L.H. / Chen, Y.C. / Tsai, L.C.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucanase
B: Glucanase
C: Glucanase
D: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,34048
Polymers141,7534
Non-polymers2,58744
Water19,6901093
1
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,41018
Polymers35,4381
Non-polymers97217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8718
Polymers35,4381
Non-polymers4337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,17014
Polymers35,4381
Non-polymers73213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8898
Polymers35,4381
Non-polymers4517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)309.859, 87.353, 82.551
Angle α, β, γ (deg.)90.000, 93.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-842-

HOH

21A-855-

HOH

31D-662-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucanase


Mass: 35438.246 Da / Num. of mol.: 4 / Fragment: UNP residues 128-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orpinomyces sp. Y102 (fungus) / Strain: Y102 / Gene: cbhC7 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A076U926, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Non-polymers , 8 types, 1137 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1093 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.93 Å3/Da / Density % sol: 68.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 6K, 0.1M ammonium phosphate buffer, 2% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 200111 / % possible obs: 98.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 / Net I/av σ(I): 23.809 / Net I/σ(I): 20.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.862.60.359186.3
1.86-1.9430.292198.7
1.94-2.033.30.222199.9
2.03-2.133.40.145199.8
2.13-2.273.40.096199.9
2.27-2.443.40.071199.9
2.44-2.693.40.052199.8
2.69-3.083.40.04199.7
3.08-3.883.30.04199.3
3.88-303.30.025199

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
HKL-2000data processing
RefinementResolution: 1.8→27.76 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 10048 5 %RANDOM
Rwork0.2091 ---
obs0.2106 190060 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.88 Å2 / Biso mean: 31.986 Å2 / Biso min: 13.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9976 0 165 1093 11234
Biso mean--44.38 40.08 -
Num. residues----1288
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 622 -
Rwork0.307 11727 -
all-12349 -
obs--84.19 %

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