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- PDB-7qfd: Crystal structure of a bacterial pyranose 2-oxidase complex with ... -

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Basic information

Entry
Database: PDB / ID: 7qfd
TitleCrystal structure of a bacterial pyranose 2-oxidase complex with D-glucose
ComponentsGMC oxidoreductase family protein
KeywordsOXIDOREDUCTASE / P2Ox / FAD / bacteria / glucose / flavoproteins
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
: / 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
FLAVIN-ADENINE DINUCLEOTIDE / alpha-D-glucopyranose / GMC oxidoreductase family protein
Similarity search - Component
Biological speciesPseudarthrobacter siccitolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBorges, P.T. / Frazao, T. / Taborda, A. / Frazao, C. / Martins, L.O.
Funding supportEuropean Union, Portugal, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionB-LigZymes H2020-MSCA-RISE 2018European Union
Foundation for Science and Technology (FCT)PTDC/BII-BBF/29564/2017 Portugal
CitationJournal: Nat Commun / Year: 2023
Title: Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms.
Authors: Taborda, A. / Frazao, T. / Rodrigues, M.V. / Fernandez-Luengo, X. / Sancho, F. / Lucas, M.F. / Frazao, C. / Melo, E.P. / Ventura, M.R. / Masgrau, L. / Borges, P.T. / Martins, L.O.
History
DepositionDec 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.country
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMC oxidoreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5826
Polymers55,3021
Non-polymers1,2805
Water52229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.256, 78.489, 150.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1327-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein GMC oxidoreductase family protein


Mass: 55301.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudarthrobacter siccitolerans (bacteria)
Gene: ARTSIC4J27_4061 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024H8G7
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 33 molecules

#2: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2 M ammonium sulfate and 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9654 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9654 Å / Relative weight: 1
ReflectionResolution: 2.35→75.11 Å / Num. obs: 18894 / % possible obs: 96.3 % / Redundancy: 5 % / CC1/2: 0.97 / Net I/σ(I): 4.11
Reflection shellResolution: 2.35→2.46 Å / Num. unique obs: 18815 / CC1/2: 0.42

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AsP2Ox WT

Resolution: 2.35→55.42 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 256 1.36 %
Rwork0.2453 18559 -
obs0.2455 18815 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.58 Å2 / Biso mean: 66.1127 Å2 / Biso min: 29.36 Å2
Refinement stepCycle: final / Resolution: 2.35→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 83 29 3571
Biso mean--61.71 47.52 -
Num. residues----458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.460.42331160.3618812892893
2.97-55.420.22821400.216897479887100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.08250.36171.44516.098-3.02016.58110.04920.1141-0.2024-0.20810.38360.7359-0.7093-0.1692-0.40850.54790.06910.08650.4229-0.05170.56628.456834.7542-23.7556
26.6654-0.3889-1.48685.21130.31492.16220.0457-0.1554-0.0986-0.64970.3330.5883-0.2439-0.3242-0.11980.5556-0.009-0.00650.47020.09710.64178.336232.5562-27.8824
37.8430.4238-0.85375.1992.98179.64830.68440.44950.4901-0.482-0.5248-0.52390.59820.6265-0.19310.68010.10270.11510.54770.12550.590320.533717.8385-35.3398
40.1315-0.22591.93023.1759-1.83445.1315-0.14320.2475-0.11960.3215-0.1358-0.5611-0.29440.54760.19090.53080.0029-0.02420.42030.03270.934421.250318.8921-17.0933
58.54311.70350.19013.9779-2.41226.9719-0.36580.6502-0.60060.77120.69632.0386-0.1517-0.6907-0.28030.61150.08220.26890.60320.29051.10590.318519.1387-13.7745
66.2724-2.83781.748.1461-3.87684.99620.16480.4621-0.5668-1.47850.4283-0.17261.2903-0.4436-0.59490.6594-0.0748-0.04850.521-0.0750.93546.5768-1.1454-17.597
71.17111.4816-2.4564.5157-4.05734.7409-0.18330.15130.1665-1.05760.46170.12060.1363-0.6641-0.11890.64790.0366-0.00640.53080.02960.77316.46138.5133-19.7553
87.50093.0321-0.93357.16980.47260.071-0.41160.4988-0.4104-0.56850.4140.1958-0.5856-0.2726-0.0530.59730.02820.00980.53270.03140.60967.741432.8366-29.6994
97.42244.0656.2094.37174.43865.7832-1.0078-0.06171.06541.73930.57421.2984-2.65790.6356-0.2061.48340.02130.16970.4410.08140.800416.877945.9094-16.1507
100.9168-0.853-0.37658.1922-2.9911.424-0.09460.0153-0.05410.6602-0.0531-0.4665-0.50170.08380.17510.652-0.06940.01160.47030.01760.636321.420630.2019-17.9595
117.9809-4.30833.00355.10681.01333.4469-0.43772.3863-3.3119-0.65540.46392.5342-0.45340.4982-0.54261.1833-0.33050.07391.1417-0.15351.659711.7543-5.7305-25.6986
125.9822.7681-0.02549.02430.49328.8713-0.46980.2768-0.53450.0820.338-0.38720.3864-0.06620.14920.36340.03190.01690.3410.08730.783317.52455.2852-11.889
135.48192.05140.9968.0215-2.8569.43070.3757-0.48951.03470.3092-1.0122-1.648-0.66051.35240.20310.6703-0.1721-0.09970.74210.11951.413731.870332.0095-15.2463
143.12764.1718-3.62268.42-3.41375.4212-0.1852-0.62890.3311.50990.4598-0.8576-0.89140.14060.00260.6614-0.101-0.30940.628-0.02061.172930.923313.9096-5.0688
156.00544.57512.12323.39191.45278.7844-0.07930.3416-1.2245-0.0861-0.3013-1.06321.55510.32490.03750.5910.0810.06460.50030.18741.105423.1344-5.628-13.0417
162.90720.9259-0.61340.4284-0.40563.1421-0.37850.6318-0.13751.497-0.2725-0.253-0.32480.31310.1190.663-0.04190.08830.47620.05750.761123.223415.8777-12.3231
170.4397-1.9629-0.24088.3085-1.52184.43240.0954-0.2523-0.06060.88730.1907-0.7348-1.22310.0024-0.1320.7996-0.0680.04740.5135-0.01040.675713.272827.8342-8.4786
187.5386-1.7671-1.13332.4985-0.61553.3122-0.39850.1294-0.27152.2810.62381.7303-0.47770.1471-0.16850.5560.08630.20140.47210.07560.8227-0.38937.9555-12.6279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:29)A5 - 29
2X-RAY DIFFRACTION2(chain A and resid 30:48)A30 - 48
3X-RAY DIFFRACTION3(chain A and resid 49:91)A49 - 91
4X-RAY DIFFRACTION4(chain A and resid 92:147)A92 - 147
5X-RAY DIFFRACTION5(chain A and resid 148:156)A148 - 156
6X-RAY DIFFRACTION6(chain A and resid 157:186)A157 - 186
7X-RAY DIFFRACTION7(chain A and resid 187:213)A187 - 213
8X-RAY DIFFRACTION8(chain A and resid 214:235)A214 - 235
9X-RAY DIFFRACTION9(chain A and resid 236:248)A236 - 248
10X-RAY DIFFRACTION10(chain A and resid 249:303)A249 - 303
11X-RAY DIFFRACTION11(chain A and resid 304:327)A304 - 327
12X-RAY DIFFRACTION12(chain A and resid 328:374)A328 - 374
13X-RAY DIFFRACTION13(chain A and resid 375:394)A375 - 394
14X-RAY DIFFRACTION14(chain A and resid 395:409)A395 - 409
15X-RAY DIFFRACTION15(chain A and resid 410:428)A410 - 428
16X-RAY DIFFRACTION16(chain A and resid 429:449)A429 - 449
17X-RAY DIFFRACTION17(chain A and resid 450:494)A450 - 494
18X-RAY DIFFRACTION18(chain A and resid 495:509)A495 - 509

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