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- PDB-4le4: Crystal structure of PaGluc131A with cellotriose -

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Basic information

Entry
Database: PDB / ID: 4le4
TitleCrystal structure of PaGluc131A with cellotriose
ComponentsBeta-glucanaseGlucanase
KeywordsHYDROLASE / glucanse / GH131
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Jelly Rolls - #1160 / Glycoside hydrolase 131, catalytic N-terminal / Glycoside hydrolase 131 catalytic N-terminal domain / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cellotriose / Beta-glucanase
Similarity search - Component
Biological speciesPodospora anserina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJiang, T. / Chan, H.C. / Huang, C.H. / Ko, T.P. / Huang, T.Y. / Liu, J.R. / Guo, R.T.
CitationJournal: To be Published
Title: Crystal Structures of a GH131 beta-Glucanase Catalytic Domain from Podospora anserina in Complex with Cellotriose
Authors: Jiang, T. / Chan, H.C. / Huang, C.H. / Ko, T.P. / Huang, T.Y. / Liu, J.R. / Guo, R.T.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
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 / struct_conn / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucanase
B: Beta-glucanase
C: Beta-glucanase
D: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3785
Polymers110,8734
Non-polymers5041
Water20,1051116
1
A: Beta-glucanase


Theoretical massNumber of molelcules
Total (without water)27,7181
Polymers27,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-glucanase


Theoretical massNumber of molelcules
Total (without water)27,7181
Polymers27,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-glucanase


Theoretical massNumber of molelcules
Total (without water)27,7181
Polymers27,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2232
Polymers27,7181
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.623, 61.854, 79.041
Angle α, β, γ (deg.)81.54, 75.16, 77.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-glucanase / Glucanase


Mass: 27718.361 Da / Num. of mol.: 4 / Fragment: UNP residues 19-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21trxB(DE3) / References: UniProt: J7K096
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 0.7M LiCl, 33% PEG6K, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 87110 / % possible obs: 97 % / Redundancy: 3.4 %
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 3 / Num. unique all: 8638 / % possible all: 95.9

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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: 4LE3

4le3


Resolution: 1.8→25 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.216 -RANDOM
Rwork0.178 --
all-89997 -
obs-84769 -
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7697 0 34 1116 8847
LS refinement shellResolution: 1.8→1.86 Å /
RfactorNum. reflection
Rfree0.304 -
Rwork0.256 -
obs-7674

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