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- PDB-4moo: Pyranose 2-oxidase H450G mutant with 2-fluorinated galactose -

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Basic information

Entry
Database: PDB / ID: 4moo
TitlePyranose 2-oxidase H450G mutant with 2-fluorinated galactose
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-galactopyranose / Pyranose 2-oxidase
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4433
Polymers70,4731
Non-polymers9702
Water9,260514
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 area24340 Å2
ΔGint-122 kcal/mol
Surface area80800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.672, 101.672, 127.562
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-GAF / 2-deoxy-2-fluoro-alpha-D-galactopyranose / 2-DEOXY-2-FLUORO-GALACTOSE / 2-deoxy-2-fluoro-alpha-D-galactose / 2-deoxy-2-fluoro-D-galactose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
a-D-Galp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
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: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→54.03 Å / Num. all: 80572 / Num. obs: 80572 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Net I/σ(I): 27.1
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 9 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 6649 / % possible all: 97.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.518 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22371 1907 2.4 %RANDOM
Rwork0.1908 ---
all0.19159 78664 --
obs0.19159 78664 99.75 %-
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: 18.353 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 65 514 5115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.024722
X-RAY DIFFRACTIONr_bond_other_d0.0010.023175
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.9646425
X-RAY DIFFRACTIONr_angle_other_deg1.06237736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1915575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60124.509224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71315758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.961527
X-RAY DIFFRACTIONr_chiral_restr0.1850.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02952
LS refinement shellResolution: 1.65→1.739 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.285 222 -
Rwork0.219 10506 -
obs--98.46 %
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)
12.3268-0.7372-1.31861.6185-0.27554.21090.02530.3181-0.1641-0.2005-0.03530.06180.2739-0.14730.010.0709-0.00590.00130.0877-0.02010.039871.225649.268419.0992
20.23250.0788-0.06520.0828-0.03530.0569-0.0152-0.0030.0026-0.010.02090.01620.0062-0.0189-0.00570.03050.00750.00390.0281-0.00320.01859.174345.972744.5419
30.3246-0.126-0.05510.37760.09340.3451-0.00350.0362-0.0159-0.04930.0078-0.0224-0.00150.0281-0.00440.0548-0.00720.010.06030.00650.045571.75756.183833.5836
42.0343-0.90150.06150.74870.01560.4936-0.04610.00870.12510.01880.01770.0313-0.05-0.11290.02850.06130.005-0.00360.06030.00890.067352.549580.683448.3999
50.2824-0.1139-0.07580.31570.11370.2799-0.01360.0159-0.0353-0.01850.0145-0.03570.01590.0248-0.00090.03340.00070.00980.03730.00070.041675.304354.275842.2609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 72
2X-RAY DIFFRACTION2A73 - 173
3X-RAY DIFFRACTION3A174 - 370
4X-RAY DIFFRACTION4A371 - 461
5X-RAY DIFFRACTION5A462 - 618

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