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- PDB-7qva: Crystal structure of a bacterial pyranose 2-oxidase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7qva
TitleCrystal structure of a bacterial pyranose 2-oxidase in complex with mangiferin
ComponentsGMC oxidoreductase family protein
KeywordsOXIDOREDUCTASE / flavoprotein / mangiferin / substrate / FAD / bacterial / pyranose-2-oxidase
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 / Mangiferin / GMC oxidoreductase family protein
Similarity search - Component
Biological speciesPseudarthrobacter siccitolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBorges, P.T. / Frazao, T. / Taborda, T. / Brissos, V. / 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
DepositionJan 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Author supporting evidence / Database references / Category: 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

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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)56,7986
Polymers55,3021
Non-polymers1,4965
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-38 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.650, 78.858, 147.348
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-1402-

HOH

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Components

#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
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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
#3: Chemical ChemComp-HZI / Mangiferin / 2-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-1,3,6,7-tetrakis(oxidanyl)xanthen-9-one


Mass: 422.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18O11 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.9 %
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: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.6→73.7 Å / Num. obs: 14110 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.985 / Net I/σ(I): 6.99
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 2229 / CC1/2: 0.495

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AsP2OX WT

Resolution: 2.6→73.67 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.49 / Stereochemistry target values: LS_WUNIT_K1
Details: THE REFINEMENT CONVERGED TO R-WORK AND R-FREE OF 0.228 AND 0.282, RESPECTIVELY, WITH A R-FREE SET OF 1414 REFLECTIONS. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET.
RfactorNum. reflection% reflection
Rfree0.2137 14108 100 %
Rwork0.2137 14108 -
obs0.2137 14108 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.97 Å2 / Biso mean: 35.4186 Å2 / Biso min: 1.81 Å2
Refinement stepCycle: final / Resolution: 2.6→73.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 98 122 3676
Biso mean--53.7 20.9 -
Num. residues----457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.630.34614470.346144789490
2.63-2.660.30124500.3012450900100
2.66-2.690.27414450.2741445890100
2.69-2.720.25454780.2545478956100
2.72-2.760.27084850.2708485970100
2.76-2.80.26144350.2614435870100
2.8-2.840.24424790.2442479958100
2.84-2.880.24014660.2401466932100
2.88-2.920.2634660.263466932100
2.92-2.970.24544590.2454459918100
2.97-3.020.23934750.2393475950100
3.02-3.080.25894620.2589462924100
3.08-3.140.2394530.239453906100
3.14-3.20.24274810.2427481962100
3.2-3.270.22744700.2274470940100
3.27-3.350.2034670.203467934100
3.35-3.430.20084700.2008470940100
3.43-3.520.19754520.1975452904100
3.52-3.630.19474830.1947483966100
3.63-3.740.19794620.1979462924100
3.74-3.880.19454720.194547294499
3.88-4.030.18784640.1878464928100
4.03-4.220.1724820.172482964100
4.22-4.440.15984700.1598470940100
4.44-4.720.15794690.1579469938100
4.72-5.080.17334900.173349098099
5.08-5.590.20094740.2009474948100
5.59-6.40.21374860.2137486972100
6.4-8.050.20814940.2081494988100
8.07-73.670.2075220.207522104498
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)
10.08920.0330.12141.03980.51540.38350.1992-0.1159-0.11980.23610.12420.39480.3901-0.3281-0.03420.215-0.1002-0.0610.18830.07570.24988.33136.159325.8454
25.0946-1.9151-0.90846.26421.75275.8052-0.5546-1.02460.94491.25290.1451-0.20530.2630.34890.28590.4084-0.0392-0.01710.3542-0.07240.262417.30423.773438.1893
36.31570.0065-2.30972.6308-2.74347.64770.54050.01390.97720.6694-0.1111-0.9451-1.04020.94090.18880.2467-0.07120.01570.3812-0.04880.507727.565520.197728.6828
40.52430.13950.56450.8160.99711.5296-0.04770.5414-0.3792-0.12770.091-0.64590.03840.87380.0620.04370.0410.12610.57930.24790.912836.699216.936116.9571
50.29280.02420.46941.7001-0.01471.4616-0.03590.03810.24290.0752-0.0904-0.30020.15030.24350.06180.1591-0.012-0.06090.17950.06660.301317.762421.870817.1571
63.74261.20180.550.9782-0.78161.66540.2871-0.1060.2706-0.3186-0.2310.6581-0.5507-0.7392-0.08840.29990.1235-0.02840.22730.05830.20361.883423.286214.399
72.72980.40690.45524.8964-1.53492.0157-0.0859-0.22840.28540.85040.13710.1419-0.5277-0.26650.01280.21610.0391-0.00230.17820.01450.23937.106239.030816.5611
80.1252-0.2530.28741.0895-0.13390.98240.0503-0.1808-0.22770.09650.05550.21840.3395-0.1995-0.05820.2308-0.083-0.00130.20.05070.29427.52557.525529.3695
93.53370.6342.02794.66974.57619.8818-0.58020.20560.1403-0.31580.38820.06590.6530.9785-0.10960.4491-0.0041-0.04180.2306-0.00240.330118.3751-4.266421.4806
101.3829-0.23980.22412.165-1.12560.90170.09220.066-0.2373-0.1086-0.1299-0.30150.34880.02190.03830.2803-0.0084-0.00570.1503-0.01560.154821.074110.303115.8684
114.2348-5.3516-5.24556.76136.62966.49980.6915-0.72110.3739-0.31510.20090.5815-0.7006-0.8417-0.64370.3488-0.12460.18990.8093-0.0430.735813.16253.970125.9109
122.218-0.9966-1.95872.9937-0.38753.9956-0.1408-0.45370.21720.4620.0548-0.0941-0.10030.36220.12420.18170.0622-0.19840.04710.16540.255314.405535.86313.6613
132.7135-0.48060.50674.0883-0.89552.61470.2455-0.1254-0.2107-0.1965-0.1414-0.36060.17620.3037-0.05440.1013-0.06510.05820.28910.08340.321827.64419.364715.0605
144.0146-0.63663.61336.9643-1.83774.0512-0.61180.24110.1746-1.01550.1243-0.49690.52310.5019-0.25650.30080.05550.17410.36420.02870.352830.384125.57033.92
154.4411-1.8164-1.87416.10190.90554.04530.3120.16250.5-0.0665-0.3266-0.0015-0.0089-0.2435-0.03390.2251-0.0673-0.09040.17550.08440.332422.306643.80911.2351
161.78040.6944-0.16422.8548-1.56461.39360.0498-0.01250.0512-0.4751-0.1924-0.17220.4931-0.22990.06860.3416-0-0.0280.18430.02120.209318.322615.84939.0534
171.6132.66110.47996.00270.72170.4944-0.11280.2815-0.3408-0.3370.50330.050.08490.0559-0.02260.2177-0.0092-0.07430.1470.06720.30154.54379.873612.6176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:52)A5 - 52
2X-RAY DIFFRACTION2(chain A and resid 53:68)A53 - 68
3X-RAY DIFFRACTION3(chain A and resid 69:98)A69 - 98
4X-RAY DIFFRACTION4(chain A and resid 99:108)A99 - 108
5X-RAY DIFFRACTION5(chain A and resid 109:141)A109 - 141
6X-RAY DIFFRACTION6(chain A and resid 142:166)A142 - 166
7X-RAY DIFFRACTION7(chain A and resid 167:210)A167 - 210
8X-RAY DIFFRACTION8(chain A and resid 211:235)A211 - 235
9X-RAY DIFFRACTION9(chain A and resid 236:253)A236 - 253
10X-RAY DIFFRACTION10(chain A and resid 254:303)A254 - 303
11X-RAY DIFFRACTION11(chain A and resid 304:308)A304 - 308
12X-RAY DIFFRACTION12(chain A and resid 325:346)A325 - 346
13X-RAY DIFFRACTION13(chain A and resid 347:395)A347 - 395
14X-RAY DIFFRACTION14(chain A and resid 396:407)A396 - 407
15X-RAY DIFFRACTION15(chain A and resid 408:426)A408 - 426
16X-RAY DIFFRACTION16(chain A and resid 427:480)A427 - 480
17X-RAY DIFFRACTION17(chain A and resid 481:509)A481 - 509

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