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- PDB-9fl2: Crystal structure of Oscillatoria princeps pyranose oxidase -

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Basic information

Entry
Database: PDB / ID: 9fl2
TitleCrystal structure of Oscillatoria princeps pyranose oxidase
Componentspyranose oxidase
KeywordsOXIDOREDUCTASE / FAD / covalent flavin
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesOscillatoria princeps RMCB-10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)H2020-NMBP-BIO-2017European Union
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Identification of a robust bacterial pyranose oxidase that displays an unusual pH dependence.
Authors: Santema, L.L. / Rozeboom, H.J. / Borger, V.P. / Kaya, S.G. / Fraaije, M.W.
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pyranose oxidase
B: pyranose oxidase
C: pyranose oxidase
D: pyranose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,09511
Polymers243,8474
Non-polymers3,2497
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, + gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28000 Å2
ΔGint-171 kcal/mol
Surface area66280 Å2
Unit cell
Length a, b, c (Å)105.971, 137.406, 143.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
pyranose oxidase


Mass: 60961.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria princeps RMCB-10 (bacteria)
Production host: Escherichia coli (E. coli) / References: pyranose oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.2 / Details: PEG3350, sodium sulfate, bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.64→99.285 Å / Num. obs: 38297 / % possible obs: 88.6 % / Redundancy: 12.8 % / CC1/2: 0.941 / Rpim(I) all: 0.106 / Rrim(I) all: 0.38 / Net I/σ(I): 7.3
Reflection shellResolution: 2.64→2.868 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1915 / CC1/2: 0.296 / Rpim(I) all: 0.727 / % possible all: 63.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→99.28 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 43.932 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25018 1922 5 %RANDOM
Rwork0.1877 ---
obs0.19086 36375 61.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-0 Å2
2---0.17 Å20 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.64→99.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16765 0 215 74 17054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01217503
X-RAY DIFFRACTIONr_bond_other_d0.0020.01615986
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.82223917
X-RAY DIFFRACTIONr_angle_other_deg0.7661.75636907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.12252099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.349588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.612102713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.22527
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220799
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024017
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6133.8178420
X-RAY DIFFRACTIONr_mcbond_other2.6133.8178420
X-RAY DIFFRACTIONr_mcangle_it4.2686.8510511
X-RAY DIFFRACTIONr_mcangle_other4.2676.8510512
X-RAY DIFFRACTIONr_scbond_it2.6844.0349083
X-RAY DIFFRACTIONr_scbond_other2.6844.0359080
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3987.29813407
X-RAY DIFFRACTIONr_long_range_B_refined7.91546.5574432
X-RAY DIFFRACTIONr_long_range_B_other7.91546.5474433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.64→2.709 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.7 10 -
Rwork0.577 186 -
obs--4.32 %
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)
10.1233-0.01120.05070.1074-0.00420.0810.00780.01270.0210.0012-0.0076-0.006-0.00440.0189-0.00010.04320.00090.0080.00490.00070.0057-1.592613.773526.9888
20.12120.02760.01660.09670.01620.10940.02480.0477-0.04630.0012-0.0053-0.0090.01150.0338-0.01950.03620.0171-0.00860.0299-0.02160.0194-3.2506-16.608311.8217
30.2130.00960.05190.1243-0.01210.09960.01580.03510.05660.00320.00160.0138-0.0087-0.0195-0.01740.03170.01020.0040.01530.01820.0265-50.609115.67989.5697
40.21930.008-0.03880.1135-0.00060.0870.0238-0.0308-0.0469-0.008-0.00710.01360.0004-0.0267-0.01670.0333-0.0019-0.01030.01770.01530.0195-52.2202-12.535728.6214
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 601
2X-RAY DIFFRACTION2B2 - 601
3X-RAY DIFFRACTION3C2 - 601
4X-RAY DIFFRACTION4D2 - 601

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