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- PDB-3ays: GH5 endoglucanase from a ruminal fungus in complex with cellotriose -

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Basic information

Entry
Database: PDB / ID: 3ays
TitleGH5 endoglucanase from a ruminal fungus in complex with cellotriose
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / Tim barrel / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellotriose / Endoglucanase
Similarity search - Component
Biological speciesPiromyces rhizinflatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsTseng, C.-W. / Ko, T.-P. / Guo, R.-T. / Liu, J.-R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Substrate binding of a GH5 endoglucanase from the ruminal fungus Piromyces rhizinflata.
Authors: Tseng, C.-W. / Ko, T.-P. / Guo, R.-T. / Huang, J.-W. / Wang, H.-C. / Huang, C.-H. / Cheng, Y.-S. / Wang, A.H.-J. / Liu, J.-R.
History
DepositionMay 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
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 / 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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8242
Polymers43,3191
Non-polymers5041
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endoglucanase
hetero molecules

A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6474
Polymers86,6392
Non-polymers1,0092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.204, 82.204, 221.856
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Endoglucanase / Cellulase


Mass: 43319.277 Da / Num. of mol.: 1 / Mutation: E154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piromyces rhizinflatus (fungus) / Gene: egla / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9URH5, cellulase
#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.: 180 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5M sodium citrate, 6mM cellotetraose, 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 315 / Detector: CCD / Date: Sep 24, 2010 / Details: Rh Coated mirrors
RadiationMonochromator: LN2-Cooled, Fixed-Exit Si(111) Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 23418 / Num. obs: 22798 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 23.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 60.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 25 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 8.3 / Num. unique all: 1110 / % possible all: 97.3

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Processing

Software
NameVersionClassification
Blu-IceControl Softwaredata collection
CNSrefinement
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3AYR

3ayr


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.62 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21826 1165 5.1 %RANDOM
Rwork0.16154 ---
all0.164 23418 --
obs0.16427 21543 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.464 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.85 Å20 Å2
2--1.69 Å20 Å2
3----2.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.187 Å0.213 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 34 180 3104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9364080
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55425.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3115491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4721513
X-RAY DIFFRACTIONr_chiral_restr0.1280.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212328
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0371.51773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.89522852
X-RAY DIFFRACTIONr_scbond_it3.35931231
X-RAY DIFFRACTIONr_scangle_it5.1414.51228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 79 -
Rwork0.189 1550 -
obs--97.14 %
Refinement TLS params.Method: refined / Origin x: -1.9275 Å / Origin y: 33.6816 Å / Origin z: -2.4566 Å
111213212223313233
T0.0127 Å20.0011 Å20.0087 Å2-0.1399 Å20.0894 Å2--0.069 Å2
L0.8928 °20.0416 °20.1877 °2-0.5987 °2-0.1041 °2--0.9654 °2
S-0.0001 Å °-0.1529 Å °-0.1587 Å °-0.0287 Å °0.0291 Å °-0.0184 Å °0.0163 Å °-0.1074 Å °-0.0291 Å °

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