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- PDB-7vkd: Reduced enzyme of FAD-dpendent Glucose Dehydrogenase at pH6.5 -

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Basic information

Entry
Database: PDB / ID: 7vkd
TitleReduced enzyme of FAD-dpendent Glucose Dehydrogenase at pH6.5
ComponentsGMC oxidoreductase
KeywordsOXIDOREDUCTASE / glucose dehydrogenase / reduced enzyme / FLAVOPROTEIN
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 oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.58 Å
AuthorsNakajima, Y. / Nishiya, Y. / Ito, K.
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
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Structure summary / Category: audit_author
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GMC oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4662
Polymers61,6781
Non-polymers7881
Water11,169620
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area19920 Å2
Unit cell
Length a, b, c (Å)94.090, 94.090, 123.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GMC oxidoreductase


Mass: 61678.102 Da / Num. of mol.: 1
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-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, Na tartrate, Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 76668 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 57.5
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 15.9 / Num. unique obs: 7559 / CC1/2: 0.994 / CC star: 0.999 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.154 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18266 3739 4.9 %RANDOM
Rwork0.15003 ---
obs0.15159 72749 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.791 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0 Å2
2--0.46 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 53 620 4957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194482
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9666121
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81224.67197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70415702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2571524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213437
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_it1.0151.3142262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5791.9712827
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8391.4712220
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.73712.6017766
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: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 257 -
Rwork0.147 5327 -
obs--100 %

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