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- PDB-3wdy: The complex structure of E113A with cellotetraose -

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Basic information

Entry
Database: PDB / ID: 3wdy
TitleThe complex structure of E113A with cellotetraose
ComponentsBeta-1,3-1,4-glucanase
KeywordsHYDROLASE / 1 / 3-1 / 4-beta-glucanase / 3(4)-beta-glucanase / PtLic16A / beta-jellyroll fold
Function / homology
Function and homology information


endo-1,3(4)-beta-glucanase / licheninase activity / glucan catabolic process / side of membrane / plasma membrane
Similarity search - Function
: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cellobiose / beta-cellotetraose / beta-D-glucopyranose / endo-1,3(4)-beta-glucanase
Similarity search - Component
Biological speciesPaecilomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsCheng, Y.S. / Huang, C.H. / Chen, C.C. / Huang, T.Y. / Ko, T.P. / Huang, J.W. / Wu, T.H. / Liu, J.R. / Guo, R.T.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Structural and mutagenetic analyses of a 1,3-1,4-beta-glucanase from Paecilomyces thermophila
Authors: Cheng, Y.S. / Huang, C.H. / Chen, C.C. / Huang, T.Y. / Ko, T.P. / Huang, J.W. / Wu, T.H. / Liu, J.R. / Guo, R.T.
History
DepositionJun 25, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-1,4-glucanase
B: Beta-1,3-1,4-glucanase
C: Beta-1,3-1,4-glucanase
D: Beta-1,3-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,52910
Polymers127,5594
Non-polymers1,9706
Water18,0871004
1
A: Beta-1,3-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2322
Polymers31,8901
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-1,3-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2322
Polymers31,8901
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-1,3-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8334
Polymers31,8901
Non-polymers9433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-1,3-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2322
Polymers31,8901
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.283, 92.311, 98.320
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-1,3-1,4-glucanase / PtLic16A


Mass: 31889.859 Da / Num. of mol.: 4 / Fragment: UNP residues 19-314 / Mutation: E113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paecilomyces (fungus) / Strain: J18 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: E0XN39, licheninase

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Sugars , 3 types, 5 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3
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
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 1005 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1004 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M sodium cacodylate, 34%(w/v) PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→25 Å / Num. obs: 97796 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.3
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.4 / Num. unique all: 9735 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDT

3wdt


Resolution: 1.94→24.67 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4682 4.8 %RANDOM
Rwork0.184 ---
all-97778 --
obs-93244 95.4 %-
Solvent computationBsol: 41.8041 Å2
Displacement parametersBiso mean: 29.2327 Å2
Baniso -1Baniso -2Baniso -3
1-3.925 Å20 Å2-2.473 Å2
2---2.299 Å20 Å2
3----1.626 Å2
Refinement stepCycle: LAST / Resolution: 1.94→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8987 0 131 1004 10122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2251.5
X-RAY DIFFRACTIONc_scbond_it1.8282
X-RAY DIFFRACTIONc_mcangle_it1.7872
X-RAY DIFFRACTIONc_scangle_it2.5432.5
LS refinement shellResolution: 1.94→2.01 Å /
RfactorNum. reflection
Rfree0.291 -
Rwork0.244 -
obs-8460

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