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- PDB-4moi: Pyranose 2-oxidase H450G/V546C double mutant with 3-fluorinated g... -

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Basic information

Entry
Database: PDB / ID: 4moi
TitlePyranose 2-oxidase H450G/V546C double mutant with 3-fluorinated glucose
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / GMC OXIDOREDUCTASE / PHBH FOLD / HOMOTETRAMER / FAD-BINDING / SUBSTRATE COMPLEX / FLAVINYLATION / INTRACELLULAR
Function / homology
Function and homology information


pyranose oxidase / pyranose oxidase activity / flavin adenine dinucleotide binding / periplasmic space
Similarity search - Function
Phage tail proteins - 2 layer sandwich fold - #50 / Pyranose 2-oxidase / Phage tail proteins - 2 layer sandwich fold / : / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / 3-deoxy-3-fluoro-beta-D-glucopyranose / Pyranose 2-oxidase
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTan, T.C. / Spadiut, O. / Gandini, R. / Haltrich, D. / Divne, C.
CitationJournal: Plos One / Year: 2014
Title: Structural Basis for Binding of Fluorinated Glucose and Galactose to Trametes multicolor Pyranose 2-Oxidase Variants with Improved Galactose Conversion.
Authors: Tan, T.C. / Spadiut, O. / Gandini, R. / Haltrich, D. / Divne, C.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8936
Polymers140,9542
Non-polymers1,9394
Water11,440635
1
A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,78712
Polymers281,9084
Non-polymers3,8798
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area22560 Å2
ΔGint-154 kcal/mol
Surface area80540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.504, 101.504, 238.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pyranose 2-oxidase / Pyranose oxidase


Mass: 70476.969 Da / Num. of mol.: 2 / Mutation: H450G, V546C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes ochracea (fungus) / Gene: p2o / Plasmid: pET21(d+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7ZA32, pyranose oxidase
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Sugar ChemComp-G3F / 3-deoxy-3-fluoro-beta-D-glucopyranose / 3-deoxy-3-fluoro-beta-D-glucose / 3-deoxy-3-fluoro-D-glucose / 3-deoxy-3-fluoro-glucose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
b-D-Glcp3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS IS A CLONING ARTIFACT

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M MES, 50 mM MgCl2, 10% (w/v) monomethylether PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.946496 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2013 / Details: unfocused
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946496 Å / Relative weight: 1
ReflectionResolution: 1.9→47.73 Å / Num. all: 98867 / Num. obs: 98867 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.175 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2000 2 %RANDOM
Rwork0.196 ---
obs0.197 96838 100 %-
all-96838 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9070 0 130 635 9835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.029442
X-RAY DIFFRACTIONr_bond_other_d0.0010.026352
X-RAY DIFFRACTIONr_angle_refined_deg2.031.96512846
X-RAY DIFFRACTIONr_angle_other_deg1.058315476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08951150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00724.509448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.167151516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5521554
X-RAY DIFFRACTIONr_chiral_restr0.1380.21402
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021904
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3 267 -
Rwork0.253 12930 -
obs--99.95 %
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)
10.2678-0.21490.17570.4749-0.21280.18780.03920.09850.0279-0.0511-0.0682-0.05810.01190.01090.02890.04060.01920.03330.10930.02110.060354.953261.230732.9758
20.4972-0.0274-0.09690.3365-0.10030.34970.02440.16590.0286-0.0854-0.0388-0.0453-0.0072-0.04210.01440.02960.02010.0090.09510.02860.04843.286470.089130.0821
31.35650.1943-0.49411.0167-0.15611.7790.04120.06280.1811-0.0207-0.0771-0.3533-0.13680.23790.03590.02190.00570.02530.09490.08380.194861.720579.682432.1878
40.98140.65040.25930.82320.00070.41560.07510.0643-0.14720.0178-0.0359-0.00680.1398-0.0913-0.03910.0572-0.0310.00560.1139-0.03420.059322.273553.829945.255
50.37160.0859-0.11060.398-0.11870.39450.0240.09710.0837-0.0459-0.0461-0.104-0.03970.00470.02210.01890.0120.01650.06740.04150.072547.588576.045838.625
60.2442-0.1481-0.20350.45270.15220.28160.02640.07380.0029-0.0116-0.04940.037-0.0028-0.05290.0230.02630.0103-0.0190.1004-0.01880.067446.129940.752134.3639
70.6890.12770.22820.42930.09420.46680.01550.033-0.0107-0.0356-0.0293-0.02340.02180.05720.01370.04280.01790.02180.1058-0.01380.055364.521233.402528.2861
81.4342-0.08410.70760.77020.18471.49580.04020.015-0.1449-0.0049-0.0180.18670.134-0.181-0.02220.0171-0.0033-0.0170.0993-0.05640.095339.225825.267927.2907
90.65340.4196-0.12540.92150.20680.42010.03780.04460.1101-0.012-0.009-0.0287-0.10110.0494-0.02880.0487-0.00540.00630.08720.0250.063677.446748.481246.5615
100.21370.14020.16930.33820.08640.41080.01980.0451-0.0542-0.038-0.02640.07640.0462-0.03760.00660.02710.0081-0.01320.0799-0.0430.087553.114725.365436.4333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 138
2X-RAY DIFFRACTION2A139 - 306
3X-RAY DIFFRACTION3A307 - 360
4X-RAY DIFFRACTION4A361 - 462
5X-RAY DIFFRACTION5A463 - 618
6X-RAY DIFFRACTION6B43 - 163
7X-RAY DIFFRACTION7B164 - 292
8X-RAY DIFFRACTION8B293 - 358
9X-RAY DIFFRACTION9B359 - 474
10X-RAY DIFFRACTION10B475 - 618

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