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- PDB-4qi3: Cytochrome domain of Myriococcum thermophilum cellobiose dehydrog... -

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Basic information

Entry
Database: PDB / ID: 4qi3
TitleCytochrome domain of Myriococcum thermophilum cellobiose dehydrogenase, MtCYT
ComponentsCellobiose dehydrogenase
KeywordsOXIDOREDUCTASE / immunoglobulin-like beta-sandwich / electron transfer / CDH dehydrogenase domain / 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 / 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 ...Cellobiose dehydrogenase, cytochrome 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / alpha-D-mannopyranose / Cellobiose dehydrogenase
Similarity search - Component
Biological speciesMyriococcum thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 2.2Apr 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
B: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,44217
Polymers44,2522
Non-polymers3,19015
Water6,305350
1
A: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7098
Polymers22,1261
Non-polymers1,5837
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7339
Polymers22,1261
Non-polymers1,6078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-47 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.405, 56.357, 73.005
Angle α, β, γ (deg.)90.00, 104.56, 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 Cellobiose dehydrogenase /


Mass: 22125.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myriococcum thermophilum (fungus) / Strain: CBS 208.89 / Gene: CDH / Plasmid: pPICZ B / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: A9XK88

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Sugars , 2 types, 10 molecules

#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 / 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
#4: 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.: 8
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

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Non-polymers , 3 types, 355 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 298 K / pH: 8.4
Details: 0.1 M Tris-HCl pH 8.4, 0.2 M MgCl2, 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2011 / Details: MIRRORS
RadiationMonochromator: CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→47.82 Å / Num. obs: 75847 / % possible obs: 99.1 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BALBES

Resolution: 1.4→44.06 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 2000 2.64 %
Rwork0.178 --
obs0.179 75847 99.2 %
all-75847 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 205 350 3667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093451
X-RAY DIFFRACTIONf_angle_d2.4834760
X-RAY DIFFRACTIONf_dihedral_angle_d14.1141230
X-RAY DIFFRACTIONf_chiral_restr0.083524
X-RAY DIFFRACTIONf_plane_restr0.006599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4350.41241410.34485221X-RAY DIFFRACTION99
1.435-1.47380.35461430.2995267X-RAY DIFFRACTION100
1.4738-1.51720.30491440.26215284X-RAY DIFFRACTION99
1.5172-1.56620.29721420.23245286X-RAY DIFFRACTION100
1.5662-1.62210.27431430.20295255X-RAY DIFFRACTION100
1.6221-1.68710.23941420.18685272X-RAY DIFFRACTION100
1.6871-1.76390.20581440.16555290X-RAY DIFFRACTION100
1.7639-1.85690.26471420.15975265X-RAY DIFFRACTION100
1.8569-1.97320.22891450.15865330X-RAY DIFFRACTION100
1.9732-2.12560.19981430.15355272X-RAY DIFFRACTION100
2.1256-2.33950.20481440.15745315X-RAY DIFFRACTION100
2.3395-2.67790.23841430.17645326X-RAY DIFFRACTION100
2.6779-3.37370.21151450.17755312X-RAY DIFFRACTION99
3.3737-44.08140.20221390.16065152X-RAY DIFFRACTION94

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