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- PDB-4qi7: Cellobiose dehydrogenase from Neurospora crassa, NcCDH -

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Basic information

Entry
Database: PDB / ID: 4qi7
TitleCellobiose dehydrogenase from Neurospora crassa, NcCDH
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


cellobiose dehydrogenase (acceptor) activity / cellulose binding / flavin adenine dinucleotide binding / carbohydrate metabolic process / hydrolase activity / 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 / 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 / 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 / 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 speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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 / Category: citation / citation_author
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
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 2.0Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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 / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)182,87147
Polymers172,4722
Non-polymers10,39945
Water00
1
A: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,96127
Polymers86,2361
Non-polymers5,72526
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,91120
Polymers86,2361
Non-polymers4,67519
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14080 Å2
ΔGint-325 kcal/mol
Surface area60710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.599, 141.851, 146.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cellobiose dehydrogenase


Mass: 86236.000 Da / Num. of mol.: 2 / Fragment: cellobiose dehydrogenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Strain: OR74A / Gene: cdh-1, NCU00206 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q7RXM0

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Sugars , 2 types, 17 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
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


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
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 , 4 types, 28 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Pt
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Mes-OH pH 6.5, 1.5 M magnesium sulfate, 0.02 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0597
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2011 / Details: MIRRORS
RadiationMonochromator: CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 2.9→58.64 Å / Num. obs: 62494 / % possible obs: 99.9 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.3_1477)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→51.04 Å / SU ML: 0.5 / σ(F): 1.36 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1994 3.19 %
Rwork0.185 --
obs0.187 62460 99.9 %
all-62460 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→51.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12040 0 442 0 12482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112821
X-RAY DIFFRACTIONf_angle_d1.65617537
X-RAY DIFFRACTIONf_dihedral_angle_d15.4694481
X-RAY DIFFRACTIONf_chiral_restr0.0581951
X-RAY DIFFRACTIONf_plane_restr0.0072229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97260.46151360.40044275X-RAY DIFFRACTION100
2.9726-3.05290.41491480.33774259X-RAY DIFFRACTION100
3.0529-3.14270.35771360.31594280X-RAY DIFFRACTION100
3.1427-3.24420.36811420.28664247X-RAY DIFFRACTION100
3.2442-3.36010.33951410.25394298X-RAY DIFFRACTION100
3.3601-3.49460.26611390.20264258X-RAY DIFFRACTION100
3.4946-3.65360.23781480.17954275X-RAY DIFFRACTION100
3.6536-3.84620.2241360.15264313X-RAY DIFFRACTION100
3.8462-4.0870.20651430.14914314X-RAY DIFFRACTION100
4.087-4.40240.15831450.12554301X-RAY DIFFRACTION100
4.4024-4.84520.16461480.12064340X-RAY DIFFRACTION100
4.8452-5.54550.19221410.14234366X-RAY DIFFRACTION100
5.5455-6.9840.19171420.18214403X-RAY DIFFRACTION100
6.984-51.04530.24281490.19114537X-RAY DIFFRACTION99
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)
10.0395-0.01730.03580.0115-0.00530.02550.0081-0.0202-0.0224-0.1840.08720.0363-0.124-0.039700.8735-0.06240.05340.68740.00520.7002129.7641-28.518162.7006
20.0240.01740.05520.0522-0.01560.07280.01190.1122-0.17230.01740.09030.02180.0374-0.07550.00840.34470.06930.06530.16670.06410.3294133.9525-2.9267166.6186
30.46720.1579-0.13220.2454-0.20330.4093-0.0889-0.1654-0.429-0.02660.0583-0.135-0.41450.0674-0.02270.18310.0633-0.04330.23450.12640.0851150.476627.9552172.4699
40.01470.0125-0.00310.01710.01130.0259-0.00460.02860.15660.03430.0796-0.00990.0721-0.0445-01.2058-0.13060.25430.98410.0940.9926167.8689-28.2147154.1353
50.02460.01-0.0153-0.00850.03850.01970.0687-0.1073-0.0554-0.1008-0.07310.0960.1246-0.026300.8178-0.06290.23310.68510.06830.7642165.8161-29.8062158.1673
60.43730.3948-0.14560.684-0.25850.42760.11250.40920.11830.68730.20710.0179-0.192-0.20080.44590.0318-0.02090.1670.10030.20590.1345151.1894-9.5942211.9655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 188 )
2X-RAY DIFFRACTION2chain 'A' and (resid 189 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 806 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 130 )
5X-RAY DIFFRACTION5chain 'B' and (resid 131 through 225 )
6X-RAY DIFFRACTION6chain 'B' and (resid 226 through 806 )

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