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- PDB-6idw: GH6 Orpinomyces sp. Y102 enzyme -

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Basic information

Entry
Database: PDB / ID: 6idw
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 superfamily / Glycosyl hydrolases family 6 / 1, 4-beta cellobiohydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / PHOSPHATE ION / Glucanase
Similarity search - Component
Biological speciesOrpinomyces sp. Y102 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsTsai, L.C. / Huang, H.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (Taiwan)NSC101-2311-B-027-001 Taiwan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of the GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo and endo activity and its complex with cellobiose.
Authors: Huang, H.C. / Qi, L.H. / Chen, Y.C. / Tsai, L.C.
History
DepositionSep 11, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 17, 2018ID: 5JX6
Revision 1.0Oct 17, 2018Provider: 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 1.2Dec 18, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)143,95218
Polymers141,7534
Non-polymers2,19914
Water6,305350
1
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0305
Polymers35,4381
Non-polymers5914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-5 kcal/mol
Surface area13830 Å2
MethodPISA
2
B: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1156
Polymers35,4381
Non-polymers6775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-7 kcal/mol
Surface area13940 Å2
MethodPISA
3
C: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0275
Polymers35,4381
Non-polymers5894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13610 Å2
MethodPISA
4
D: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7812
Polymers35,4381
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)310.369, 86.594, 82.314
Angle α, β, γ (deg.)90.000, 93.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-613-

HOH

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Glucanase / / cellobiohydrolase and cellotrihydrolase


Mass: 35438.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orpinomyces sp. Y102 (fungus) / Gene: cbhC7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A076U926, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 360 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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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: 3.89 Å3/Da / Density % sol: 68.41 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→154.87 Å / Num. obs: 52523 / % possible obs: 97.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.055 / Χ2: 1.051 / Net I/σ(I): 29.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.8-2.93.70.24750871.055194.6
2.9-3.023.80.18750691.082195.1
3.02-3.1540.14151671.015195.5
3.15-3.324.30.10952781.056198.2
3.32-3.534.50.08353121.056198.9
3.53-3.84.60.06353101.099198.8
3.8-4.184.60.05353441.016198.9
4.18-4.784.50.04953321.075198.4
4.78-6.024.50.04353421.057198.3
6.02-104.40.03352821.004195.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JX5

5jx5


Resolution: 2.78→154.87 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.848 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.34 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1934 3.8 %RANDOM
Rwork0.22 ---
obs0.2212 48646 92.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.34 Å2 / Biso mean: 32.426 Å2 / Biso min: 3.76 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.78→154.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9976 0 145 350 10471
Biso mean--40.02 25.84 -
Num. residues----1288
LS refinement shellResolution: 2.782→2.854 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 88 -
Rwork0.276 2549 -
all-2637 -
obs--65.6 %

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