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- PDB-6rwf: The dissociation mechanism of processive cellulases -

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Basic information

Entry
Database: PDB / ID: 6rwf
TitleThe dissociation mechanism of processive cellulases
ComponentsGlucanase
KeywordsHYDROLASE / Cellobiogydrolase I / Cel7A from Hypocrea jecorina
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / 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
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsStahlberg, J. / Knott, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC36-08GO28308 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: The dissociation mechanism of processive cellulases.
Authors: Vermaas, J.V. / Kont, R. / Beckham, G.T. / Crowley, M.F. / Gudmundsson, M. / Sandgren, M. / Stahlberg, J. / Valjamae, P. / Knott, B.C.
History
DepositionJun 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Mar 11, 2020Group: Data collection / Polymer sequence / Refinement description
Category: chem_comp / entity_poly / refine
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _refine.pdbx_diffrn_id
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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_ptnr1_label_alt_id / _struct_conn.pdbx_role / _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_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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Mar 30, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3247
Polymers45,8091
Non-polymers5166
Water12,250680
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-31 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.363, 51.632, 65.590
Angle α, β, γ (deg.)90.000, 96.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucanase


Mass: 45808.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (strain QM6a) (fungus)
Strain: QM6a / Gene: cel7a, TRIREDRAFT_123989 / Production host: Trichoderma reesei QM6a (fungus)
References: UniProt: G0RVK1, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 mM sodium acetate, pH 5.0, 20% PEG 5000 monomethyl ether, 0.1 M MES pH 6.0, 10 mM cobalt chloride, 12.5% glycerol.
PH range: 5 - 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.967 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 6, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.64→40.48 Å / Num. obs: 44198 / % possible obs: 97.5 % / Redundancy: 1.6 % / Net I/σ(I): 8.9
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 1.5 % / Num. unique obs: 2624 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CEL

6cel


Resolution: 1.64→29.52 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 2127 5.1 %RANDOM
Rwork0.1269 ---
obs0.1288 39479 91.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.96 Å2 / Biso mean: 7.707 Å2 / Biso min: 0.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.02 Å2
2--0.26 Å20 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 1.64→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 19 680 3901
Biso mean--21.91 20.67 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133408
X-RAY DIFFRACTIONr_bond_other_d0.0380.0182795
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.654672
X-RAY DIFFRACTIONr_angle_other_deg2.5311.5756585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.0795.328473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18725.098153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98615484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.462157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024375
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02693
X-RAY DIFFRACTIONr_mcbond_it0.9470.6681783
X-RAY DIFFRACTIONr_mcbond_other0.9440.6661782
X-RAY DIFFRACTIONr_mcangle_it1.5391.0022243
LS refinement shellResolution: 1.636→1.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.174 166 -
Rwork0.146 2624 -
all-2790 -
obs--82.23 %

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