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- PDB-4mof: Pyranose 2-oxidase H450G mutant with 2-fluorinated glucose -

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Basic information

Entry
Database: PDB / ID: 4mof
TitlePyranose 2-oxidase H450G mutant with 2-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 / 2-deoxy-2-fluoro-alpha-D-glucopyranose / Pyranose 2-oxidase
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 6, 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

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Assembly

Deposited unit
A: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4433
Polymers70,4731
Non-polymers9702
Water11,205622
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)285,77112
Polymers281,8924
Non-polymers3,8798
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area24190 Å2
ΔGint-134 kcal/mol
Surface area81530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.340, 102.340, 128.510
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: 70472.961 Da / Num. of mol.: 1 / Mutation: H450G
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-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
a-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
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: MAX II / Beamline: I911-3 / Wavelength: 0.96 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 3, 2008 / Details: Rh-coated Si mirrors
RadiationMonochromator: Double-crystal monochromator, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.85→54.42 Å / Num. all: 58446 / Num. obs: 58446 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Net I/σ(I): 17.4
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4176 / % possible all: 93.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.253 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19353 1796 3.1 %RANDOM
Rwork0.15819 ---
all0.15929 56649 --
obs0.15929 56649 99.36 %-
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: 20.663 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 0 65 622 5199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.024698
X-RAY DIFFRACTIONr_bond_other_d0.0010.023161
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9646393
X-RAY DIFFRACTIONr_angle_other_deg1.04237700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42724.484223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23615752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.451527
X-RAY DIFFRACTIONr_chiral_restr0.1750.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02950
LS refinement shellResolution: 1.85→1.95 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.252 212 -
Rwork0.197 7374 -
obs--96.34 %
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)
10.23830.0711-0.04670.16-0.130.2069-0.00230.0223-0.0007-0.02260.0020.00770.0117-0.00240.00030.03830.00120.00630.0336-0.01160.026662.163147.304239.7882
20.3225-0.1878-0.11790.5930.20660.34620.03220.04450.0385-0.0523-0.0225-0.0221-0.06760.0144-0.00970.0556-0.00890.01720.06150.01710.030170.380764.461732.4235
30.978-0.188-0.23841.35520.1240.91960.02870.0608-0.1897-0.0254-0.0340.00020.15660.11460.00530.05250.02040.01060.0271-0.02490.066677.59738.287132.3887
41.2765-0.7516-0.02490.8348-0.08270.4275-0.00530.03940.1050.0042-0.00620.0639-0.0739-0.09820.01150.0552-0.0078-0.00190.0513-0.0010.058754.054478.639849.7689
50.3874-0.141-0.10770.34210.16470.41740.00390.0239-0.0381-0.02370.005-0.03820.02070.0543-0.00890.0399-0.00420.00980.0440.00080.046177.04353.752142.0317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 173
2X-RAY DIFFRACTION2A174 - 293
3X-RAY DIFFRACTION3A294 - 356
4X-RAY DIFFRACTION4A357 - 469
5X-RAY DIFFRACTION5A470 - 618

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