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- PDB-7vzs: FAD-dpendent Glucose Dehydrogenase complexed with an inhibitor at... -

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Basic information

Entry
Database: PDB / ID: 7vzs
TitleFAD-dpendent Glucose Dehydrogenase complexed with an inhibitor at pH7.56
ComponentsGMC oxidoreductase
KeywordsOXIDOREDUCTASE / glucose dehydrogenase / reduced enzyme / FLAVOPROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / 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
D-glucal / FLAVIN-ADENINE DINUCLEOTIDE / GMC oxidoreductase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 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)127,24218
Polymers123,3562
Non-polymers3,88616
Water13,277737
1
A: GMC oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7139
Polymers61,6781
Non-polymers2,0358
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GMC oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5299
Polymers61,6781
Non-polymers1,8518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.933, 67.079, 150.681
Angle α, β, γ (deg.)90.00, 97.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 10 molecules AB

#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
#3: Sugar
ChemComp-DGO / D-glucal


Type: D-saccharide / Mass: 146.141 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H10O4 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 745 molecules

#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
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.56
Details: PEG 10000, HEPES Na buffer, soaking a crystal in a crystallization solution containing 1 M D-glucal

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 92885 / % possible obs: 95.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.4
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 9552

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.218 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19033 4611 5 %RANDOM
Rwork0.15236 ---
obs0.15425 88008 95.28 %-
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: 21.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.15 Å2
2---0.04 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8620 0 258 737 9615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9812482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09651154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32824.682393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.076151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4021547
X-RAY DIFFRACTIONr_chiral_restr0.0910.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216909
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_it0.6881.55649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25729064
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96233503
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1234.53407
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: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 326 -
Rwork0.182 6670 -
obs--98.13 %

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