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- PDB-8hdd: Complex structure of catalytic, small, and a partial electron tra... -

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Basic information

Entry
Database: PDB / ID: 8hdd
TitleComplex structure of catalytic, small, and a partial electron transfer subunits from Burkholderia cepacia FAD glucose dehydrogenase
Components
  • Glucose dehydrogenase
  • Glucose dehydrogenase beta subunit
  • Twin-arginine translocation pathway signal
KeywordsOXIDOREDUCTASE / Glucose dehydrogenase / FAD / Burkholderia cepacia / cytochrome c / HEM
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / 3 iron, 4 sulfur cluster binding / flavin adenine dinucleotide binding / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane
Similarity search - Function
FAD-containing D-sorbitol dehydrogenase small subunit / Membrane bound FAD containing D-sorbitol dehydrogenase / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / : / : / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Glucose-methanol-choline oxidoreductase, C-terminal ...FAD-containing D-sorbitol dehydrogenase small subunit / Membrane bound FAD containing D-sorbitol dehydrogenase / Membrane-bound alcohol dehydrogenase, cytochrome c subunit / : / : / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Twin-arginine translocation pathway signal / Glucose dehydrogenase beta subunit / Glucose dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYoshida, H. / Sode, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other privateNA (sponsorship research) Japan
Citation
Journal: Commun Biol / Year: 2022
Title: Microgravity environment grown crystal structure information based engineering of direct electron transfer type glucose dehydrogenase.
Authors: Okuda-Shimazaki, J. / Yoshida, H. / Lee, I. / Kojima, K. / Suzuki, N. / Tsugawa, W. / Yamada, M. / Inaka, K. / Tanaka, H. / Sode, K.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein.
Authors: Yoshida, H. / Kojima, K. / Shiota, M. / Yoshimatsu, K. / Yamazaki, T. / Ferri, S. / Tsugawa, W. / Kamitori, S. / Sode, K.
History
DepositionNov 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose dehydrogenase
B: Glucose dehydrogenase beta subunit
C: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4566
Polymers124,7583
Non-polymers1,6983
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-95 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.015, 71.797, 114.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Glucose dehydrogenase


Mass: 59906.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GB:AAN39686.1 / Source: (gene. exp.) Burkholderia cepacia (bacteria) / Gene: gdhAlpha / Plasmid: pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GQE7, EC: 1.1.5.9
#2: Protein Glucose dehydrogenase beta subunit


Mass: 51796.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GB:AAQ06608.1 / Source: (gene. exp.) Burkholderia cepacia (bacteria) / Plasmid: plasmid / Details (production host): pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q71JE9
#3: Protein Twin-arginine translocation pathway signal


Mass: 13053.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GB:CAZ78686.1 / Source: (gene. exp.) Burkholderia cepacia (bacteria) / Gene: BMULJ_04411 / Plasmid: plasmid / Details (production host): pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KLY3

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 5.6 / Details: tacsimate, PEG 3350, DDM, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 34334 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.179 / Net I/σ(I): 10.34
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3-3.080.73224430.9610.7911
3.08-3.160.64624630.9650.6981
3.16-3.250.50323760.9740.5441
3.25-3.350.40722800.9840.441
3.35-3.460.33322670.9870.3611
3.46-3.590.25821600.9920.2811
3.59-3.720.2220770.9920.2411
3.72-3.870.21320230.9940.231
3.87-4.050.15519360.9970.1671
4.05-4.240.13118920.9980.1421
4.24-4.470.11617630.9980.1261
4.47-4.740.09716780.9980.1051
4.74-5.070.10815890.9970.1171
5.07-5.480.10314840.9970.1141
5.48-60.11213860.9980.1211
6-6.710.10412450.9970.1131
6.71-7.750.07311060.9980.081
7.75-9.490.059670.9990.0541
9.49-13.420.0337520.9990.0361
13.42-500.0344710.0331

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
REFMAC5.8.0258refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A2U

6a2u


Resolution: 3→49.88 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.876 / SU B: 94.265 / SU ML: 0.633 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32335 1725 5 %RANDOM
Rwork0.27531 ---
obs0.27778 32619 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.33 Å2
Baniso -1Baniso -2Baniso -3
1--7.01 Å2-0 Å2-0 Å2
2---5.86 Å20 Å2
3---12.87 Å2
Refinement stepCycle: 1 / Resolution: 3→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5935 0 103 0 6038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136202
X-RAY DIFFRACTIONr_bond_other_d00.0175679
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.6678450
X-RAY DIFFRACTIONr_angle_other_deg1.0211.58213190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.155765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.24522.182307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.74315989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.431540
X-RAY DIFFRACTIONr_chiral_restr0.0280.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021271
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_it2.937.983069
X-RAY DIFFRACTIONr_mcbond_other2.937.983068
X-RAY DIFFRACTIONr_mcangle_it4.80811.9613831
X-RAY DIFFRACTIONr_mcangle_other4.80811.9613832
X-RAY DIFFRACTIONr_scbond_it2.458.0623133
X-RAY DIFFRACTIONr_scbond_other2.448.0623131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.93712.0324613
X-RAY DIFFRACTIONr_long_range_B_refined7.18295.9637427
X-RAY DIFFRACTIONr_long_range_B_other7.18395.9657428
X-RAY DIFFRACTIONr_rigid_bond_restr3.352311881
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 116 -
Rwork0.415 2327 -
obs--99.71 %

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