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- PDB-6a2u: Crystal structure of gamma-alpha subunit complex from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 6a2u
TitleCrystal structure of gamma-alpha subunit complex from Burkholderia cepacia FAD glucose dehydrogenase
Components
  • Glucose dehydrogenase
  • Twin-arginine translocation pathway signal
KeywordsSIGNALING PROTEIN/OXIDOREDUCTASE / Glucose dehydrogenase / FAD / Burkholderia cepacia / OXIDOREDUCTASE / SIGNALING PROTEIN-OXIDOREDUCTASE complex
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide 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 / Twin-arginine translocation pathway signal / Glucose dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYoshida, H. / Kojima, K. / Yoshimatsu, K. / Shiota, M. / Yamazaki, T. / Ferri, S. / Tsugawa, W. / Kamitori, S. / Sode, K.
CitationJournal: 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
DepositionJun 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)149,7428
Polymers147,5794
Non-polymers2,1634
Water3,171176
1
A: Twin-arginine translocation pathway signal
B: Glucose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8714
Polymers73,7902
Non-polymers1,0812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-57 kcal/mol
Surface area23860 Å2
MethodPISA
2
C: Twin-arginine translocation pathway signal
D: Glucose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8714
Polymers73,7902
Non-polymers1,0812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-54 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.521, 110.521, 524.877
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Twin-arginine translocation pathway signal


Mass: 13053.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Plasmid: pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KLY3*PLUS
#2: Protein Glucose dehydrogenase


Mass: 60735.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence of Twin-arginine translocation pathway signal was deposited to Genbank with accession ...Sequence of Twin-arginine translocation pathway signal was deposited to Genbank with accession number CAZ78686.

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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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 60005 / % possible obs: 99.9 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.034 / Rrim(I) all: 0.154 / Χ2: 1.099 / Net I/σ(I): 7.3 / Num. measured all: 1273970
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6421.40.42829200.9790.0940.4391.138100
2.64-2.6921.50.37429570.9840.0820.3841.168100
2.69-2.7421.40.3428990.9870.0750.3481.188100
2.74-2.821.50.31929210.9880.0710.3271.176100
2.8-2.8621.50.28429500.9890.0630.2911.213100
2.86-2.9321.40.26329390.9880.0580.271.196100
2.93-321.50.22929310.9930.050.2351.123100
3-3.0821.50.21429630.9930.0470.2191.125100
3.08-3.1721.60.19629350.9940.0430.2011.052100
3.17-3.2821.50.17529530.9950.0390.1791.083100
3.28-3.3921.60.15729580.9950.0350.1611.022100
3.39-3.5321.50.14929850.9950.0330.1521.08100
3.53-3.6921.50.14330090.9940.0320.1471.076100
3.69-3.8821.50.13729550.9960.030.141.052100
3.88-4.1321.50.13230170.9950.0290.1351.057100
4.13-4.4521.40.12730330.9890.0280.131.109100
4.45-4.8921.30.12330410.9920.0280.1260.985100
4.89-5.621.10.1230940.9950.0270.1231.098100
5.6-7.0520.70.12231450.9940.0280.1260.976100
7.05-5018.20.1234000.9920.0290.1241.07199.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The structure of selenomethionine variant

Resolution: 2.6→43.74 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.896 / SU B: 10.412 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.294
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 3023 5.1 %RANDOM
Rwork0.2039 ---
obs0.2068 56812 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 174.52 Å2 / Biso mean: 42.678 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.6→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10022 0 120 176 10318
Biso mean--31.61 29.79 -
Num. residues----1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01910420
X-RAY DIFFRACTIONr_bond_other_d00.029800
X-RAY DIFFRACTIONr_angle_refined_deg0.5741.98114188
X-RAY DIFFRACTIONr_angle_other_deg0.4633.00122608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.12651284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2923.867450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.308151678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4471568
X-RAY DIFFRACTIONr_chiral_restr0.040.21538
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.02111704
X-RAY DIFFRACTIONr_gen_planes_other00.022298
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 201 -
Rwork0.275 4078 -
all-4279 -
obs--99.19 %

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