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- PDB-1naa: Cellobiose Dehydrogenase Flavoprotein Fragment in Complex with Ce... -

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Basic information

Entry
Database: PDB / ID: 1naa
TitleCellobiose Dehydrogenase Flavoprotein Fragment in Complex with Cellobionolactam
ComponentsCellobiose dehydrogenase
KeywordsOXIDOREDUCTASE / GMC oxidoreductase / alpha/beta structure / rossmann fold / PHBH fold / product analogue complex / 6-hydroxylated FAD
Function / homology
Function and homology information


cellobiose dehydrogenase (acceptor) / cellobiose dehydrogenase (acceptor) activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / cellulose catabolic process / flavin adenine dinucleotide binding / extracellular region / metal ion binding
Similarity search - Function
DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Cellobiose dehydrogenase, cytochrome domain / Cytochrome domain of cellobiose dehydrogenase / Cholesterol Oxidase; domain 2 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / NAD(P)-binding Rossmann-like domain / Glucose-methanol-choline oxidoreductase, N-terminal ...DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Cellobiose dehydrogenase, cytochrome domain / Cytochrome domain of cellobiose dehydrogenase / Cholesterol Oxidase; domain 2 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / NAD(P)-binding Rossmann-like domain / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE / Chem-ABL / Cellobiose dehydrogenase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsHallberg, B.M. / Henriksson, G. / Pettersson, G. / Vasella, A. / Divne, C.
Citation
Journal: J.BIOL.CHEM. / Year: 2003
Title: Mechanism of the reductive half-reaction in cellobiose dehydrogenase
Authors: Hallberg, B.M. / Henriksson, G. / Pettersson, G. / Vasella, A. / Divne, C.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the flavoprotein domain of the extracellular flavocytochrome cellobiose dehydrogenase
Authors: Hallberg, B.M. / Henriksson, G. / Pettersson, G. / Divne, C.
History
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: 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

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Assembly

Deposited unit
A: Cellobiose dehydrogenase
B: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,47811
Polymers115,0902
Non-polymers3,3889
Water18,1411007
1
A: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3496
Polymers57,5451
Non-polymers1,8045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1285
Polymers57,5451
Non-polymers1,5834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.952, 185.952, 81.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Cellobiose dehydrogenase / / CDH / Cellobiose-quinone oxidoreductase


Mass: 57544.973 Da / Num. of mol.: 2 / Fragment: c-terminal flavoprotein fragment / Source method: isolated from a natural source / Source: (natural) Phanerochaete chrysosporium (fungus) / Strain: K3
References: UniProt: Q01738, cellobiose dehydrogenase (acceptor)
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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
#3: Chemical ChemComp-6FA / 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE


Mass: 801.549 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O16P2
#4: Sugar ChemComp-ABL / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside / 5-amino-5-deoxy-cellobiono-1,5-lactam / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucoside / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl D-glucoside / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl glucoside


Type: D-saccharide / Mass: 339.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21NO10
IdentifierTypeProgram
5-amino-5-deoxy-cellobiono-1,5-lactamIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1007 / 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: 2.07 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, dioxane, mes, cellobionolactam, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃ / Details: Hallberg, B.M., (2002) J.Mol.Biol., 315, 421.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
310 %(v/v)dioxane1reservoir
4100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.8→57 Å / Num. all: 98043 / Num. obs: 95043 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.5 / % possible all: 85.4
Reflection
*PLUS
Lowest resolution: 57 Å / Num. measured all: 376799
Reflection shell
*PLUS
% possible obs: 85.4 %

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1KDG

1kdg


Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.185 1894 random
Rwork0.146 --
obs0.146 93130 -
all-95024 -
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8134 0 224 1007 9365
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.022
X-RAY DIFFRACTIONr_angle_refined_deg1.92
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.92

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