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- PDB-8grj: Crystal structure of gamma-alpha subunit complex from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 8grj
TitleCrystal structure of gamma-alpha subunit complex from Burkholderia cepacia FAD glucose dehydrogenase in complex with gluconolactone
Components
  • Glucose dehydrogenase
  • twin-arginine translocation pathway signal
KeywordsOXIDOREDUCTASE / Glucose dehydrogenase / FAD / Burkholderia cepacia / SIGNALING PROTEIN-OXIDOREDUCTASE complex
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 / metal ion binding
Similarity search - Function
FAD-containing D-sorbitol dehydrogenase small subunit / Membrane bound FAD containing D-sorbitol dehydrogenase / 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 / 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 / D-glucono-1,5-lactone / Twin-arginine translocation pathway signal / Glucose dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYoshida, H. / Kojima, K. / Tsugawa, W. / Okuda-Shimazaki, J. / Kerrigan, J.A. / Sode, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other privatesponsorship research (Arkray Inc.) Japan
Citation
Journal: To Be Published
Title: Crystal structure of gamma-alpha subunit complex from Burkholderia cepacia FAD glucose dehydrogenase in complex with gluconolactone
Authors: Yoshida, H. / Kojima, K. / Tsugawa, W. / Okuda-Shimazaki, J. / Kerrigan, J.A. / 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
DepositionSep 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: twin-arginine translocation pathway signal
B: Glucose dehydrogenase
C: twin-arginine translocation pathway signal
D: Glucose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,95110
Polymers157,4324
Non-polymers2,5196
Water2,684149
1
A: twin-arginine translocation pathway signal
B: Glucose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9765
Polymers78,7162
Non-polymers1,2593
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-50 kcal/mol
Surface area23920 Å2
MethodPISA
2
C: twin-arginine translocation pathway signal
D: Glucose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9765
Polymers78,7162
Non-polymers1,2593
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-48 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.235, 111.235, 527.106
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein twin-arginine translocation pathway signal


Mass: 17980.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GB:CAZ78686.1 / Source: (gene. exp.) Burkholderia cepacia (bacteria) / Strain: ATCC 17616 / 249 / Gene: BMULJ_04411 / Plasmid: pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KLY3
#2: Protein Glucose dehydrogenase


Mass: 60735.762 Da / Num. of mol.: 2
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

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Sugars , 1 types, 2 molecules

#5: Sugar ChemComp-LGC / D-glucono-1,5-lactone / (3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE / GLUCONOLACTONE / Glucono delta-lactone


Type: D-saccharide / Mass: 178.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 3 types, 153 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→100 Å / Num. obs: 42134 / % possible obs: 99.4 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.113 / Χ2: 0.955 / Net I/σ(I): 7.4 / Num. measured all: 653811
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.95-316.30.42420550.7671100
3-3.0616.10.3920350.771100
3.06-3.1116.10.36720810.7831100
3.11-3.1816.10.31520580.7841100
3.18-3.2515.90.27220560.8141100
3.25-3.32160.20820760.8361100
3.32-3.4115.90.1920540.8731100
3.41-3.515.80.16221010.8641100
3.5-3.615.80.14520740.9091100
3.6-3.7215.70.1321100.9141100
3.72-3.8515.80.11420660.945199.9
3.85-415.50.09820950.9911100
4-4.1915.40.08420911.052199.9
4.19-4.4115.30.07621141.056199.8
4.41-4.6815.10.07121241.077199.6
4.68-5.0415.10.06721181.103199.5
5.04-5.5515.10.0721500.972199.6
5.55-6.3614.90.06621630.95199.4
6.36-8.01150.05922291.057198.8
8.01-10013.60.05422841.651193

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A2U

6a2u


Resolution: 2.95→50.04 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.846 / SU B: 16.465 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 2125 5.1 %RANDOM
Rwork0.1982 ---
obs0.2018 39931 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.89 Å2 / Biso mean: 37.59 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.95→50.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10032 0 144 149 10325
Biso mean--30.96 22.83 -
Num. residues----1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310454
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179588
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.65814236
X-RAY DIFFRACTIONr_angle_other_deg1.1871.57722290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8751286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92522.046518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.209151678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3381568
X-RAY DIFFRACTIONr_chiral_restr0.0660.21366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211658
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022134
LS refinement shellResolution: 2.95→3.022 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.339 162 -
Rwork0.262 2798 -
obs--98.11 %

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