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- PDB-7vzp: FAD-dpendent Glucose Dehydrogenase from Aspergillus oryzae -

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Basic information

Entry
Database: PDB / ID: 7vzp
TitleFAD-dpendent Glucose Dehydrogenase from Aspergillus oryzae
ComponentsGMC oxidoreductase
KeywordsOXIDOREDUCTASE / glucose dehydrogenase / reduced enzyme / FLAVOPROTEIN
Function / homology
Function and homology information


glucose oxidase / beta-D-glucose oxidase activity / 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
FLAVIN-ADENINE DINUCLEOTIDE / glucose oxidase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.2 Å
AuthorsNakajima, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24780106 Japan
CitationJournal: To Be Published
Title: Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5
Authors: Nakajima, Y.
History
DepositionNov 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMC oxidoreductase
B: GMC oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,35710
Polymers123,3562
Non-polymers3,0018
Water26,8781492
1
A: GMC oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1785
Polymers61,6781
Non-polymers1,5004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GMC oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1785
Polymers61,6781
Non-polymers1,5004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.715, 67.237, 151.312
Angle α, β, γ (deg.)90.00, 97.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GMC oxidoreductase


Mass: 61678.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: OAory_01010120 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S9DW10
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1492 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.56 / Details: PEG 10000, HEPES Na buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 318404 / % possible obs: 97.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.573 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 33
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.42 / Num. unique obs: 30785

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.481 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16916 16069 5 %RANDOM
Rwork0.15712 ---
obs0.15772 302246 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20.21 Å2
2---0.24 Å20 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8609 0 202 1492 10303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229102
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.97512404
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07851170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81524.691388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.791151421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6551547
X-RAY DIFFRACTIONr_chiral_restr0.0840.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216907
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5391.55666
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99129105
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47333436
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3174.53279
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 1113 -
Rwork0.196 21434 -
obs--94.25 %

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