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- PDB-1kdg: Crystal structure of the flavin domain of cellobiose dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1kdg
TitleCrystal structure of the flavin domain of cellobiose dehydrogenase
Componentscellobiose dehydrogenase
KeywordsOXIDOREDUCTASE / GMC oxidoreductase / PHBH fold / alpha/beta structure / Rossmann fold / 6-hydroxylated FAD
Function / homology
Function and homology information


cellobiose dehydrogenase (acceptor) / cellobiose dehydrogenase (acceptor) activity / cellulose catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / 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 / 2-(ETHYLMERCURI-THIO)-BENZOIC ACID / : / alpha-D-mannopyranose / Cellobiose dehydrogenase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsHallberg, B.M. / Henriksson, G. / Pettersson, G. / Divne, C.
CitationJournal: 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 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 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 / _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.ptnr1_symmetry / _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.ptnr2_symmetry
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)121,61924
Polymers116,0012
Non-polymers5,61822
Water20,1771120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-98 kcal/mol
Surface area36510 Å2
MethodPISA
2
A: cellobiose dehydrogenase
B: cellobiose dehydrogenase
hetero molecules

A: cellobiose dehydrogenase
B: cellobiose dehydrogenase
hetero molecules

A: cellobiose dehydrogenase
B: cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,85772
Polymers348,0036
Non-polymers16,85466
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area30560 Å2
ΔGint-887 kcal/mol
Surface area104140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.075, 185.075, 81.034
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingrhombohedral
Space group name H-MH3
DetailsTHE BIOLOGICAL ASSEMBLY IS A MONOMERIC FLAVOCYTOCHROME CONSISTING OF A B-TYPE CYTOCHROME DOMAIN LINKED TO A FLAVODEHYDROGENASE DOMAIN

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein cellobiose dehydrogenase / / E.C.1.1.3.25, E.C.1.1.5.1 / CDH / CELLOBIOSE-QUINONE OXIDOREDUCTASE /


Mass: 58000.473 Da / Num. of mol.: 2 / Fragment: C-terminal flavoprotein domain / Source method: isolated from a natural source / Details: secreted / Source: (natural) Phanerochaete chrysosporium (fungus) / Strain: K3
References: UniProt: Q01738, cellobiose dehydrogenase (acceptor)

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Sugars , 2 types, 9 molecules

#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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: Sugar
ChemComp-MAN / alpha-D-mannopyranose / Mannose


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 , 5 types, 1133 molecules

#4: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Hg
#5: Chemical ChemComp-6FA / 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE


Mass: 801.549 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O16P2
#6: Chemical ChemComp-EMT / 2-(ETHYLMERCURI-THIO)-BENZOIC ACID


Mass: 382.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10HgO2S
#7: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1120 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: AMMONIUM SULFATE, DIOXANE, MES, MERTHIOLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K
Crystal grow
*PLUS
Temperature: 15 ℃
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: MAX II / Beamline: I711 / Wavelength: 0.996 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 17, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 165042 / Num. obs: 165042 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.7
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.2 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 385729 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
MLPHAREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→23 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.169 2459 1.5 %random
Rwork0.133 ---
all0.135 165023 --
obs0.135 165023 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.5→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 243 1120 9529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.021
X-RAY DIFFRACTIONr_angle_refined_deg1.9
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0.036
RfactorNum. reflection% reflection
Rfree0.259 199 -
Rwork0.202 --
obs-12146 99.2 %
Refinement
*PLUS
Lowest resolution: 23 Å / Num. reflection obs: 162564 / Rfactor Rwork: 0.134
Solvent computation
*PLUS
Displacement parameters
*PLUS

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