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- PDB-4ynt: Crystal structure of Aspergillus flavus FAD glucose dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 4ynt
TitleCrystal structure of Aspergillus flavus FAD glucose dehydrogenase
ComponentsGlucose oxidase, putative
KeywordsOXIDOREDUCTASE / Glucose dehydrogenase / FAD
Function / homology
Function and homology information


glucose oxidase / oxidoreductase activity, acting on CH-OH group of donors / secondary metabolite biosynthetic process / flavin adenine dinucleotide binding
Similarity search - Function
Glucose Oxidase, domain 2 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / glucose oxidase
Similarity search - Component
Biological speciesAspergillus flavus NRRL3357 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsYoshida, H. / Sakai, G. / Kojima, K. / Kamitori, S. / Sode, K.
CitationJournal: Sci Rep / Year: 2015
Title: Structural analysis of fungus-derived FAD glucose dehydrogenase
Authors: Yoshida, H. / Sakai, G. / Mori, K. / Kojima, K. / Kamitori, S. / Sode, K.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Glucose oxidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3362
Polymers61,5491
Non-polymers7881
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.907, 64.359, 76.166
Angle α, β, γ (deg.)90.000, 101.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucose oxidase, putative / glucose dehydrogenase


Mass: 61548.922 Da / Num. of mol.: 1 / Fragment: UNP residues 24-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus NRRL3357 (mold) / Strain: NRRL 3357 / Gene: AFLA_076820 / Plasmid: pET30c / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: B8MX95, EC: 1.1.5.9
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BisTris, 20-25 % PEG 3350 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 45130 / % possible obs: 99 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.071 / Χ2: 1.381 / Net I/av σ(I): 17.424 / Net I/σ(I): 15.2 / Num. measured all: 143309
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.77-1.82.40.4622.421021.0993.4
1.8-1.832.80.41922411.15698.3
1.83-1.8730.33822211.24999.1
1.87-1.9130.30922731.2899
1.91-1.9530.2622311.40199
1.95-1.9930.2322561.44799.2
1.99-2.0430.18922231.37399
2.04-2.130.16722371.46199
2.1-2.1630.14422951.51899.3
2.16-2.233.10.13422381.47599.2
2.23-2.313.20.11822501.46499.2
2.31-2.43.20.10722541.40599.4
2.4-2.513.20.09422631.47699.4
2.51-2.643.30.0822641.43699.4
2.64-2.813.40.07422841.45699.5
2.81-3.033.50.06422631.41199.6
3.03-3.333.60.05922861.35799.7
3.33-3.813.60.05523031.26999.8
3.81-4.83.40.05122851.39899.8
4.8-503.70.05423611.36299.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CF3

1cf3


Resolution: 1.78→48.75 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.602 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2279 5.1 %RANDOM
Rwork0.1533 42833 --
obs0.1556 42833 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.45 Å2 / Biso mean: 23.958 Å2 / Biso min: 11.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.78→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 53 470 4855
Biso mean--16.86 30.55 -
Num. residues----570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194510
X-RAY DIFFRACTIONr_bond_other_d0.0010.024248
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9666154
X-RAY DIFFRACTIONr_angle_other_deg0.62639759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0115577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12924.694196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09615710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9241524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215210
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021030
LS refinement shellResolution: 1.775→1.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 138 -
Rwork0.231 2799 -
all-2937 -
obs--87.8 %

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