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- PDB-4v20: The 3-D structure of the cellobiohydrolase, Cel7A, from Aspergill... -

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Basic information

Entry
Database: PDB / ID: 4v20
TitleThe 3-D structure of the cellobiohydrolase, Cel7A, from Aspergillus fumigatus, disaccharide complex
ComponentsCELLOBIOHYDROLASE
KeywordsHYDROLASE / CELLULASE / BIOFUELS / CARBOHYDRATE-ACTIVE ENZYME / THERMAL STABILITY
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region
Similarity search - Function
1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. ...1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
2-deoxy-2-fluoro-beta-D-cellobiose / ACETATE ION / Probable 1,4-beta-D-glucan cellobiohydrolase B
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMoroz, O.V. / Maranta, M. / Shaghasi, T. / Harris, P.V. / Wilson, K.S. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: The Three-Dimensional Structure of the Cellobiohydrolase Cel7A from Aspergillus Fumigatus at 1.5 A Resolution
Authors: Moroz, O.V. / Maranta, M. / Shaghasi, T. / Harris, P.V. / Wilson, K.S. / Davies, G.J.
History
DepositionOct 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Data collection
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 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_conn_angle / struct_asym / 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_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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 2024Group: 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: CELLOBIOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9527
Polymers47,1381
Non-polymers8146
Water13,169731
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.560, 130.780, 46.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CELLOBIOHYDROLASE / BETA-GLUCANCELLOBIOHYDROLASE B / EXOCELLOBIOHYDROLASE B / EXOGLUCANASE B


Mass: 47137.566 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ASPERGILLUS ORYZAE (mold)
References: UniProt: Q4WM08, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 344.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2-deoxy-2-fluoro-beta-D-cellobiose
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*F][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp2fluoro]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 735 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 % / Description: NONE
Crystal growDetails: 20% PEG6K, 10 MM ZNCL2, MES PH 6.0, SEEDING OF LIGAND COMPLEX DROPS WITH NATIVE SEEDS

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorDate: Aug 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→43.49 Å / Num. obs: 73170 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V1Z
Resolution: 1.5→43.49 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.107 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15829 3869 5 %RANDOM
Rwork0.13201 ---
obs0.13334 73170 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.654 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 47 731 4066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193799
X-RAY DIFFRACTIONr_bond_other_d0.0020.023278
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9375234
X-RAY DIFFRACTIONr_angle_other_deg1.06937627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06925.839161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15215574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.174158
X-RAY DIFFRACTIONr_chiral_restr0.1110.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024656
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02882
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_it1.1531.4131983
X-RAY DIFFRACTIONr_mcbond_other1.1331.411982
X-RAY DIFFRACTIONr_mcangle_it1.6862.1182545
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8581.5441816
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.505→1.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 243 -
Rwork0.219 5338 -
obs--99.52 %

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