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- PDB-7vkf: Reduced enzyme of FAD-dpendent Glucose Dehydrogenase complex with... -

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Basic information

Entry
Database: PDB / ID: 7vkf
TitleReduced enzyme of FAD-dpendent Glucose Dehydrogenase complex with D-glucono-1,5-lactone at pH8.5
ComponentsGMC oxidoreductase
KeywordsOXIDOREDUCTASE / glucose dehydrogenase / reduced enzyme / substrate complex / 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 / D-glucono-1,5-lactone / glucose oxidase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 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)62,9264
Polymers61,6781
Non-polymers1,2483
Water9,836546
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-2 kcal/mol
Surface area19780 Å2
Unit cell
Length a, b, c (Å)95.421, 95.421, 123.841
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: Sugar ChemComp-LGC / D-glucono-1,5-lactone / (3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE / GLUCONOLACTONE


Type: D-saccharide / Mass: 178.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, Na tartrate, Bis-Tris propane buffer pH 8.5

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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: 1.6→50 Å / Num. obs: 75995 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 46.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 7468 / CC1/2: 0.976 / % 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: 1.6→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.381 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18752 3706 4.9 %RANDOM
Rwork0.15786 ---
obs0.1593 72087 99.92 %-
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: 18.685 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0 Å2
2--0.49 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 84 546 4934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.976168
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66524.718195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55915703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4691523
X-RAY DIFFRACTIONr_chiral_restr0.1780.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213432
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_it1.3771.6122272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1042.4122839
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.271.8082248
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.05514.8627735
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: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 254 -
Rwork0.176 5237 -
obs--100 %

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