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- PDB-1ocb: Structure of the wild-type cellobiohydrolase Cel6A from Humicolas... -

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Basic information

Entry
Database: PDB / ID: 1ocb
TitleStructure of the wild-type cellobiohydrolase Cel6A from Humicolas insolens in complex with a fluorescent substrate
ComponentsCELLOBIOHYDROLASE II
KeywordsHYDROLASE / CELLULOSE DEGRADATION / CELLOBIOHYDROLASE / CELLULASE / GLYCOSIDE HYDROLASE FAMILY 6 / PROCESSIVE MECHANISM
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
FLUORESCEINYLTHIOUREIDO / Exoglucanase-6A
Similarity search - Component
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVarrot, A. / Frandsen, T.P. / Von Ossowski, I. / Boyer, V. / Driguez, H. / Schulein, M. / Davies, G.J.
CitationJournal: Structure / Year: 2003
Title: Structural Basis for Ligand Binding and Processivity in Cellobiohydrolase Cel6A from Humicola Insolens
Authors: Varrot, A. / Frandsen, T.P. / Von Ossowski, I. / Boyer, V. / Driguez, H. / Schulein, M. / Davies, G.J.
History
DepositionFeb 7, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jun 24, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_database_status / pdbx_validate_chiral / struct_conn
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 / _chem_comp.type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 13, 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 / pdbx_validate_chiral
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLOBIOHYDROLASE II
B: CELLOBIOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,55111
Polymers80,0292
Non-polymers3,5219
Water12,881715
1
A: CELLOBIOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5585
Polymers40,0151
Non-polymers1,5444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLOBIOHYDROLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9926
Polymers40,0151
Non-polymers1,9785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.763, 155.681, 51.218
Angle α, β, γ (deg.)90.00, 118.42, 90.00
Int Tables number4
Space group name H-MP1211

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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, RESIDUES 89-450
Source method: isolated from a genetically manipulated source
Details: N-LINKED N-ACETYLGLUCOSAMINE ON RESIDUE ASN 141 / Source: (gene. exp.) HUMICOLA INSOLENS (fungus)
Plasmid: UNDER CONTROL OF THE FUNGAL AMYLASE PROMOTER AND AMYLOGLUCOSIDASE TERMINATOR
Production host: ASPERGILLUS ORYZAE (mold)
References: UniProt: Q9C1S9*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 3 types, 6 molecules

#2: Polysaccharide 4-amino-4-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)- ...4-amino-4-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-methyl 4-thio-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 695.685 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5][a2122h-1a_1-5_4*N]/1-2-2-3/a4-b1*S*_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp4N]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-methyl 4-thio-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 534.530 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5]/1-2-2/a4-b1*S*_b4-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp4SH]{[(4+S)][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

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Non-polymers , 3 types, 718 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FLG / FLUORESCEINYLTHIOUREIDO


Mass: 434.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H18N2O5S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O

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Details

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 HENCE THIS ENTRY BEGINS AT RESIDUE ASN 90. THIS PROTEIN IS CLOSELY RELATED TO AVICELASE 2 (SWISS-PROT ACCESSION ID:Q9C1S9) WITH WHICH IT HAS 96% SEQUENCE IDENTITY.

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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: 2.1 Å3/Da / Density % sol: 41.7 %
Crystal growpH: 4.6
Details: THE PROTEIN WAS CONCENTRATED IN WATER TO 7 MG/ML IT WAS INCUBATED 1H PRIOR CRYSTALLISATION WITH THE 5MM OF THE SUBSTRATE 16% PEG5KMME AND 200 MM CALCIUM ACETATE WERE USED AS PRECIPITANT AND ...Details: THE PROTEIN WAS CONCENTRATED IN WATER TO 7 MG/ML IT WAS INCUBATED 1H PRIOR CRYSTALLISATION WITH THE 5MM OF THE SUBSTRATE 16% PEG5KMME AND 200 MM CALCIUM ACETATE WERE USED AS PRECIPITANT AND 100 MM SODIUM ACETATE PH 4.6 AS BUFFER.
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1reservoirpH7.0
2200 mMcalcium acetate1reservoir
318 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 69418 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 6 / % possible all: 91.3
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 40 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 91.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVW

2bvw


Resolution: 1.75→38.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.877 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.168 3394 5 %RANDOM
Rwork0.133 ---
obs0.135 63815 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20.25 Å2
2---1.26 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 230 715 6575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216073
X-RAY DIFFRACTIONr_bond_other_d0.0020.025176
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9678320
X-RAY DIFFRACTIONr_angle_other_deg0.911312044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026713
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021209
X-RAY DIFFRACTIONr_nbd_refined0.2210.21149
X-RAY DIFFRACTIONr_nbd_other0.2550.26063
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.23347
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2500
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7961.53620
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34825823
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.33132453
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.54.52497
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 252
Rwork0.147 4393
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56180.05950.08660.95990.0831.05520.02040.0248-0.0568-0.06160.0263-0.0360.1350.0103-0.04680.0155-0.0066-0.01740.0437-0.00040.02291.10.1993.04
20.8781-0.0815-0.18811.4555-0.10610.7922-0.0046-0.03650.14010.14910.07450.0529-0.0562-0.0165-0.06990.00410.00520.00650.0518-0.00160.0619-33.35538.618-22.275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A90 - 450
2X-RAY DIFFRACTION2B91 - 450
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.172 / Rfactor Rwork: 0.135
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.62

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