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- PDB-4qi6: Cellobiose dehydrogenase from Myriococcum thermophilum, MtCDH -

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Basic information

Entry
Database: PDB / ID: 4qi6
TitleCellobiose dehydrogenase from Myriococcum thermophilum, MtCDH
ComponentsCellobiose dehydrogenase
KeywordsOXIDOREDUCTASE / immunoglobulin-like beta-sandwich (cytochrome) / FAD/NAD(P)-binding domain (dehydrogenase domain) / cellobiose oxidizing / electron transfer / lignocellulose degradation / cellobiose / LPMO
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / cellulose binding / polysaccharide catabolic process / flavin adenine dinucleotide binding / extracellular region / metal ion binding
Similarity search - Function
Cellobiose dehydrogenase, cytochrome domain / Cytochrome domain of cellobiose dehydrogenase / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / FAD-dependent oxidoreductase 2, FAD binding domain / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain ...Cellobiose dehydrogenase, cytochrome domain / Cytochrome domain of cellobiose dehydrogenase / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / FAD-dependent oxidoreductase 2, FAD binding domain / 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 / FAD binding domain / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / alpha-D-mannopyranose / Cellobiose dehydrogenase
Similarity search - Component
Biological speciesMyriococcum thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTan, T.C. / Gandini, R. / Sygmund, C. / Kittl, R. / Haltrich, D. / Ludwig, R. / Hallberg, B.M. / Divne, C.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.
Authors: Tan, T.C. / Kracher, D. / Gandini, R. / Sygmund, C. / Kittl, R. / Haltrich, D. / Hallberg, B.M. / Ludwig, R. / Divne, C.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Apr 3, 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: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,85812
Polymers86,6711
Non-polymers3,18811
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.151, 156.151, 85.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cellobiose dehydrogenase /


Mass: 86670.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myriococcum thermophilum (fungus) / Strain: CBS 208.89 / Gene: CDH / Plasmid: pPICZalphaB / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: A9XK88
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#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.: 4
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-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
Sequence detailsPYROGLUTAMIC ACID PCA FORMED FROM GLN

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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: 3 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 298 K / pH: 5
Details: 0.1 M ammonium sulfate, 0.4 M sodium formate, 30% (w/v) PEG monomethylether 5000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2011 / Details: MIRRORS
RadiationMonochromator: CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.2→46.353 Å / Num. obs: 17929 / % possible obs: 99.9 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1477)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED CYTOCHROM AND DEHYDROGENASE DOMAIN

Resolution: 3.2→46.35 Å / SU ML: 0.46 / σ(F): 2 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1793 10 %
Rwork0.215 --
obs0.221 17928 99.9 %
all-17928 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 207 0 6262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066445
X-RAY DIFFRACTIONf_angle_d1.2328822
X-RAY DIFFRACTIONf_dihedral_angle_d11.1292279
X-RAY DIFFRACTIONf_chiral_restr0.032974
X-RAY DIFFRACTIONf_plane_restr0.0041134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.28660.36471360.31071217X-RAY DIFFRACTION100
3.2866-3.38330.38411340.30531212X-RAY DIFFRACTION100
3.3833-3.49250.36561360.28481218X-RAY DIFFRACTION100
3.4925-3.61720.32181340.26381212X-RAY DIFFRACTION100
3.6172-3.7620.28941340.23651211X-RAY DIFFRACTION100
3.762-3.93310.31981370.22551234X-RAY DIFFRACTION100
3.9331-4.14040.28321370.20861234X-RAY DIFFRACTION100
4.1404-4.39960.22641350.1951218X-RAY DIFFRACTION100
4.3996-4.7390.21661410.17451258X-RAY DIFFRACTION100
4.739-5.21530.24881380.17661237X-RAY DIFFRACTION100
5.2153-5.96860.29341380.21251253X-RAY DIFFRACTION100
5.9686-7.51470.2711430.22091276X-RAY DIFFRACTION100
7.5147-46.35820.24371500.19951355X-RAY DIFFRACTION100

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