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- PDB-7qf8: Crystal structure of a bacterial pyranose 2-oxidase from Pseudoar... -

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Basic information

Entry
Database: PDB / ID: 7qf8
TitleCrystal structure of a bacterial pyranose 2-oxidase from Pseudoarthrobacter siccitolerans
ComponentsGMC oxidoreductase family protein
KeywordsOXIDOREDUCTASE / P2Ox / FAD / bacteria / glucose / flavoprotein
Function / homologyoxidoreductase activity, acting on CH-OH group of donors / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily / flavin adenine dinucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / GMC oxidoreductase family protein
Function and homology information
Biological speciesPseudarthrobacter siccitolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.009 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 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 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 1.2Feb 7, 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)56,4986
Polymers55,3021
Non-polymers1,1965
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-42 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.448, 78.796, 151.313
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-1175-

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 BL21(DE3) (bacteria) / References: UniProt: A0A024H8G7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
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: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2→39.4 Å / Num. obs: 31572 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 43.93 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.57
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 5031 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (18-SEP-2020)refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MIF

4mif


Resolution: 2.009→39.4 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 495 1.57 %RANDOM
Rwork0.1985 ---
obs0.1992 31571 99.8 %-
Displacement parametersBiso max: 107.55 Å2 / Biso mean: 52.32 Å2 / Biso min: 29.09 Å2
Baniso -1Baniso -2Baniso -3
1-13.6321 Å20 Å20 Å2
2---16.7931 Å20 Å2
3---3.1611 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.009→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3701 0 76 232 4009
Biso mean--51.41 53.47 -
Num. residues----494
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1295SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes709HARMONIC5
X-RAY DIFFRACTIONt_it3856HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3383SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3899HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5359HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion15.17
LS refinement shellResolution: 2.01→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.3552 26 1.98 %
Rwork0.332 1290 -
all0.3325 1316 -
obs--97.57 %
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)
12.2977-0.4048-0.29561.2348-0.68431.57470.0948-0.23120.1760.10850.01250.2128-0.0992-0.1603-0.1073-0.1120.05430.0498-0.1049-0.0003-0.19426.029330.983664.1742
212.48493.63264.10233.3963-5.130325.4783-0.7477-1.16090.65321.10960.1317-0.8612-0.41130.72730.616-0.0410.212-0.0440.0599-0.0315-0.327925.009124.369776.6803
38.7072-0.5676-0.10980.65820.9531.1004-0.1486-0.6171-1.37630.3871-0.2509-0.04220.70030.32460.3995-0.06120.14390.0634-0.09540.2215-0.157424.645411.728170.2084
43.6660.1912-1.56981.4880.14271.52860.04890.0742-0.12720.0817-0.03950.0069-0.098-0.1543-0.0094-0.21020.03260.0003-0.21850.0165-0.244620.48921.991754.902
55.4267-5.8206-4.56591.5734-2.48927.5944-0.4103-1.48271.43651.06780.2082-1.0472-0.76291.2650.2021-0.1376-0.165-0.0922-0.0678-0.1260.102642.20534.308460.495
61.6512.1231-2.90910.00060.04899.74060.272-0.37350.1026-0.148-0.2163-0.2022-0.68440.5308-0.0557-0.0793-0.02050.0613-0.24160.0208-0.128140.090731.528947.747
74.75784.56867.25060.3144-4.613331.0102-0.0843-2.17421.37841.5293-0.3064-0.2083-2.17690.96970.39070.1762-0.00040.01470.3735-0.2158-0.135228.174533.984669.2917
823.4952-4.67035.89033.9633-3.01190.82930.0165-0.66790.41230.2783-0.00680.163-0.5115-0.1845-0.0097-0.08280.05090.0813-0.1908-0.023-0.23812.538836.742767.4462
94.4742-0.49170.3534.18431.80385.38860.11670.1743-0.19870.2483-0.10450.39420.0998-0.5701-0.0122-0.3173-0.00140.0781-0.09370.0056-0.2007-2.051724.169261.1902
106.1901-0.9169-1.2880.99550.07341.2369-0.08420.2614-0.4466-0.0024-0.1040.13040.1052-0.20.1882-0.1929-0.0113-0.0004-0.19540.0189-0.227712.424218.486856.2121
11011.00824.53240.0563-7.246810.6373-0.2188-0.9736-0.01370.39110.26720.9675-0.0642-0.7316-0.04830.0282-0.08990.03530.2076-0.1713-0.004940.225229.831369.3036
121.96970.844-0.82042.1425-0.77442.26340.0077-0.13860.01010.07080.0521-0.23150.04110.7343-0.0598-0.15440.06520.0183-0.13570.0056-0.161334.720123.788253.2601
135.0842-5.85241.17510.5945-1.38458.3706-0.2318-2.17691.07660.50460.2341-0.17860.7360.6635-0.0023-0.002-0.2134-0.28980.50430.3072-0.061146.076120.532368.6402
147.25561.1884-2.13342.4168-0.49562.7625-0.33550.9419-1.0455-0.22450.07340.30.2949-0.47980.2621-0.1873-0.01030.0275-0.2488-0.0938-0.066715.20799.865749.7708
1525.11776.37248.49754.69212.68917.3245-0.27830.7581-0.6159-0.5890.0493-0.606-0.19950.28070.229-0.09280.05410.1128-0.24140.03-0.177336.517513.375843.2093
165.7735-1.1665-1.69761.07440.08471.04140.10470.6317-0.1328-0.0653-0.1212-0.1164-0.127-0.29420.0166-0.14140.0318-0.0006-0.1160.0204-0.277918.972923.139748.9801
1716.412-11.284910.38294.5024-3.21450.6401-0.0950.6321-0.0614-0.07280.11120.46740.569-0.5346-0.0162-0.15390.09150.1296-0.18840.1311-0.0737-4.40441.574252.3105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - 52 }A5 - 52
2X-RAY DIFFRACTION2{ A|53 - 61 }A53 - 61
3X-RAY DIFFRACTION3{ A|62 - 90 }A62 - 90
4X-RAY DIFFRACTION4{ A|91 - 161 }A91 - 161
5X-RAY DIFFRACTION5{ A|162 - 176 }A162 - 176
6X-RAY DIFFRACTION6{ A|177 - 197 }A177 - 197
7X-RAY DIFFRACTION7{ A|198 - 209 }A198 - 209
8X-RAY DIFFRACTION8{ A|210 - 224 }A210 - 224
9X-RAY DIFFRACTION9{ A|225 - 249 }A225 - 249
10X-RAY DIFFRACTION10{ A|250 - 307 }A250 - 307
11X-RAY DIFFRACTION11{ A|308 - 324 }A308 - 324
12X-RAY DIFFRACTION12{ A|325 - 351 }A325 - 351
13X-RAY DIFFRACTION13{ A|352 - 363 }A352 - 363
14X-RAY DIFFRACTION14{ A|364 - 401 }A364 - 401
15X-RAY DIFFRACTION15{ A|402 - 417 }A402 - 417
16X-RAY DIFFRACTION16{ A|418 - 500 }A418 - 500
17X-RAY DIFFRACTION17{ A|501 - 511 }A501 - 511

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