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- PDB-5o59: Cellobiohydrolase Cel7A from T. atroviride -

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Basic information

Entry
Database: PDB / ID: 5o59
TitleCellobiohydrolase Cel7A from T. atroviride
ComponentsGlucanase
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / CELLOBIOHYDROLASE / CELLULASE
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase activity / cellulose binding / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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
alpha-D-glucopyranose / 1-thio-beta-D-glucopyranose / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Glucanase
Similarity search - Component
Biological speciesHypocrea atroviridis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.75 Å
AuthorsBorisova, A.S. / Stahlberg, J. / Hansson, H.
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum.
Authors: Borisova, A.S. / Eneyskaya, E.V. / Jana, S. / Badino, S.F. / Kari, J. / Amore, A. / Karlsson, M. / Hansson, H. / Sandgren, M. / Himmel, M.E. / Westh, P. / Payne, C.M. / Kulminskaya, A.A. / Stahlberg, J.
History
DepositionJun 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Data collection / Polymer sequence / Category: chem_comp / entity_poly
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Glucanase
B: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,39726
Polymers90,6292
Non-polymers3,76824
Water15,295849
1
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,09912
Polymers45,3141
Non-polymers1,78511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,29814
Polymers45,3141
Non-polymers1,98313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.850, 71.340, 102.912
Angle α, β, γ (deg.)90.00, 89.99, 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 Glucanase


Mass: 45314.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hypocrea atroviridis (fungus) / Strain: ATCC 20476 / IMI 206040
References: UniProt: G9NTY1, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Sugars , 3 types, 14 molecules

#2: 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.: 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
#6: Sugar
ChemComp-GS1 / 1-thio-beta-D-glucopyranose / 1-thio-beta-D-glucose / 1-thio-D-glucose / 1-thio-glucose


Type: D-saccharide, beta linking / Mass: 196.221 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O5S
IdentifierTypeProgram
b-D-Glcp1SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#7: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 859 molecules

#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 45.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Precipitant: 5 mM NiCl2 0.1 M HEPES pH 7.0 20% w/v PEG 3350 Sample in 20 mM Bis-Tris buffer, pH 7.0 Mixing 1:1
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97243 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 1.75→58.63 Å / Num. obs: 81328 / % possible obs: 83.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.8
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.504 / Num. unique obs: 9257 / % possible all: 79.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALA3.3.16data scaling
PHASERphasing
RefinementResolution: 1.75→58.63 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19015 3413 5.1 %RANDOM
Rwork0.15606 ---
obs0.1578 63799 82.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.75→58.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 221 849 7414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026946
X-RAY DIFFRACTIONr_bond_other_d00.025714
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9649533
X-RAY DIFFRACTIONr_angle_other_deg3.9893.0113453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64925.679287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70215949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6431514
X-RAY DIFFRACTIONr_chiral_restr0.0780.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027947
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021357
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_it0.7961.7593566
X-RAY DIFFRACTIONr_mcbond_other0.7921.7593565
X-RAY DIFFRACTIONr_mcangle_it1.3592.6394496
X-RAY DIFFRACTIONr_mcangle_other1.362.6394497
X-RAY DIFFRACTIONr_scbond_it0.8571.8743380
X-RAY DIFFRACTIONr_scbond_other0.8561.8743380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3972.7765038
X-RAY DIFFRACTIONr_long_range_B_refined3.94322.1988030
X-RAY DIFFRACTIONr_long_range_B_other3.71521.7037835
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.752→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 261 -
Rwork0.258 4416 -
obs--78.11 %

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