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- PDB-2bvw: CELLOBIOHYDROLASE II (CEL6A) FROM HUMICOLA INSOLENS IN COMPLEX WI... -

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Basic information

Entry
Database: PDB / ID: 2bvw
TitleCELLOBIOHYDROLASE II (CEL6A) FROM HUMICOLA INSOLENS IN COMPLEX WITH GLUCOSE AND CELLOTETRAOSE
ComponentsCELLOBIOHYDROLASE II
KeywordsHYDROLASE / CELLULOSE DEGRADATION / CELLOBIOHYDROLASE / CELLULASE / GLYCOSIDE HYDROLASE FAMILY 6
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
Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / 1, 4-beta cellobiohydrolase / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily ...Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / 1, 4-beta cellobiohydrolase / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellotetraose / alpha-cellotriose / beta-D-glucopyranose / Exoglucanase-6A
Similarity search - Component
Biological speciesHumicola insolens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVarrot, A. / Davies, G.J. / Schulein, M.
CitationJournal: Biochemistry / Year: 1999
Title: Structural changes of the active site tunnel of Humicola insolens cellobiohydrolase, Cel6A, upon oligosaccharide binding.
Authors: Varrot, A. / Schulein, M. / Davies, G.J.
History
DepositionFeb 18, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 25, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 25, 2019Group: Advisory / Data collection / Derived calculations
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 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: CELLOBIOHYDROLASE II
B: CELLOBIOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,64715
Polymers80,0292
Non-polymers2,61813
Water11,115617
1
A: CELLOBIOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,63510
Polymers40,0151
Non-polymers1,6219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLOBIOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0125
Polymers40,0151
Non-polymers9984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.560, 154.430, 51.040
Angle α, β, γ (deg.)90.00, 119.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.51751, -0.05441, 0.85394), (-0.04213, -0.99839, -0.03809), (0.85464, -0.01627, -0.51897)
Vector: -35.10673, 38.94375, -23.87365)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CELLOBIOHYDROLASE II / CELLULASE / CEL6A


Mass: 40014.512 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE DOMAIN
Source method: isolated from a genetically manipulated source
Details: N-LINKED N-ACETYLGLUCOSAMINE ON RESIDUE ASN 141 / Source: (gene. exp.) Humicola insolens (fungus) / Description: FULL-LENGTH ENZYME OVER-EXPRESSED
Plasmid: UNDER CONTROL OF THE FUNGAL AMYLASE PROMOTER AND AMYLOGLUCOSIDASE TERMINATOR
Production host: Aspergillus oryzae (mold)
References: UniProt: Q9C1S9, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 4 types, 6 molecules

#2: 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
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-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: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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, 624 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsCELLOTETRAOSE WITH ALPHA AND BETA OXYGENE AT C1 CELLOTRIOSE WITH ALPHA AND BETA OXYGENE AT C1 ...CELLOTETRAOSE WITH ALPHA AND BETA OXYGENE AT C1 CELLOTRIOSE WITH ALPHA AND BETA OXYGENE AT C1 GLUCOSE WITH ALPHA AND BETA OXYGENE AT C1 BETA N-LINKED
Sequence detailsTHERE IS A PRO-SEQUENCE OF 23 AMINO-ACIDS WHICH ARE POST-TRANSLATIONALLY CLEAVED TO YIELD A MATURE ...THERE IS A PRO-SEQUENCE OF 23 AMINO-ACIDS WHICH ARE POST-TRANSLATIONALLY CLEAVED TO YIELD A MATURE PROTEIN OF 450 RESIDUES. THE NUMBERING OF THE PROTEIN STRUCTURE ASSUMES THAT RESIDUE 1 IS THE FIRST RESIDUE OF THE MATURE PROTEIN AND HENCE DOES NOT INCLUDE THE LEADER SEQUENCE IN THE NUMBERING. ALSO, THIS STRUCTURE IS OF THE CATALYTIC CORE DOMAIN ONLY, WHICH COMMENCES AT RESIDUE TYR 89. IN THE CHAIN A THE FIRST RESIDUE OF THE CORE IS DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY, HENCE THIS ENTRY BEGINS AT RESIDUE ASN 90. IN THE CHAIN B ASN 90 IS DISORDERED SO IT BEGINS AT GLY 91.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.2 %
Description: SEARCH MODEL WAS CEL6A FROM HUMICOLA INSOLENS NATIVE STRUCTURE
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop contains a 50:50(v/v) mix of protein and of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
119 mg/mlprotein1drop
220 mMbeta-D-cellobiose1reservoir
3200 mMammonium acetate1reservoir
4100 mMsodium acetate1reservoir
530 %PEG40001reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 1998 / Details: TORROIDAL MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 72987 / % possible obs: 89.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 11.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.359 / % possible all: 89.6
Reflection shell
*PLUS
% possible obs: 89.6 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CCP4refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BVW

1bvw


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3313 5 %RANDOM
Rwork0.175 ---
all-65198 --
obs-72987 89.6 %-
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 173 617 6412
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0240.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.260.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5493
X-RAY DIFFRACTIONp_mcangle_it2.0825
X-RAY DIFFRACTIONp_scbond_it2.4494
X-RAY DIFFRACTIONp_scangle_it3.4016
X-RAY DIFFRACTIONp_plane_restr0.01880.03
X-RAY DIFFRACTIONp_chiral_restr0.1050.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2340.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1210.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor14.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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