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- PDB-4mog: Pyranose 2-oxidase V546C mutant with 3-fluorinated glucose -

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Basic information

Entry
Database: PDB / ID: 4mog
TitlePyranose 2-oxidase V546C 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 / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / 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: 2 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5283
Polymers70,5581
Non-polymers9702
Water7,404411
1
A: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,11112
Polymers282,2324
Non-polymers3,8798
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area22710 Å2
ΔGint-160 kcal/mol
Surface area81520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.507, 102.507, 128.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Pyranose 2-oxidase / Pyranose oxidase


Mass: 70558.070 Da / Num. of mol.: 1 / Mutation: 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.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Sugar ChemComp-G3F / 3-deoxy-3-fluoro-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
b-D-Glcp3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1M MES, 50mM 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: PSI 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: 2→48.11 Å / Num. all: 46860 / Num. obs: 46860 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26.5 % / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 24.9 % / Mean I/σ(I) obs: 3.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.799 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 962 2.1 %RANDOM
Rwork0.186 ---
obs0.187 45898 99.8 %-
all-45898 --
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: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---1 Å20 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 2→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 65 411 4993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024701
X-RAY DIFFRACTIONr_bond_other_d0.0010.023164
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.9636392
X-RAY DIFFRACTIONr_angle_other_deg1.00737704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48324.464224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14915753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4351527
X-RAY DIFFRACTIONr_chiral_restr0.1310.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02948
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: 2→2.11 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 117 -
Rwork0.257 6025 -
obs--99.27 %
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)
11.514-0.18160.10691.493-0.10191.07850.023-0.13280.02980.10730.03720.0674-0.0057-0.0444-0.06020.0794-0.01280.00480.0663-0.01530.020716.8551.12-22.2601
20.1624-0.12920.05110.1664-0.15830.3169-0.00750.0110.01070.00960.02180.0146-0.0013-0.016-0.01430.0583-0.0128-0.00260.0580.00050.03418.23195.3374-47.7725
30.42880.15840.07280.45590.11390.320.0189-0.04630.0250.0691-0.0021-0.03210.00310.0282-0.01680.09060.0051-0.00960.0920.00550.060621.0605-5.4419-34.0001
42.30791.0726-0.07661.1394-0.01490.4621-0.02530.0313-0.1169-0.01480.00810.09060.055-0.10970.01720.1026-0.00130.00330.09340.01150.08641.8403-29.9365-48.7021
50.39110.18580.13360.38360.09010.36940.0027-0.01730.0520.040.0076-0.0389-0.00870.0482-0.01030.0659-0.0004-0.00220.068-0.00230.06424.6564-3.5202-42.7286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 85
2X-RAY DIFFRACTION2A86 - 172
3X-RAY DIFFRACTION3A173 - 370
4X-RAY DIFFRACTION4A371 - 461
5X-RAY DIFFRACTION5A462 - 618

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