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- PDB-4moq: Pyranose 2-oxidase V546C mutant with 2-fluorinated galactose -

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Basic information

Entry
Database: PDB / ID: 4moq
TitlePyranose 2-oxidase V546C 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
2-deoxy-2-fluoro-beta-D-galactopyranose / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Pyranose 2-oxidase
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.1Jul 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 1.2Nov 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)143,4338
Polymers141,1162
Non-polymers2,3176
Water20,4471135
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)286,86616
Polymers282,2324
Non-polymers4,63412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area25140 Å2
ΔGint-117 kcal/mol
Surface area81710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.724, 101.724, 251.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Pyranose 2-oxidase / Pyranose oxidase


Mass: 70558.070 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Sugar ChemComp-2FG / 2-deoxy-2-fluoro-beta-D-galactopyranose / 2-FLUORO-2-DEOXY-BETA-D-GALACTOPYRANOSE / 2-deoxy-2-fluoro-beta-D-galactose / 2-deoxy-2-fluoro-D-galactose / 2-deoxy-2-fluoro-galactose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
b-D-Galp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1135 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013 / Details: Rh coated meridionally focussing mirror
RadiationMonochromator: Fixed-exit LN2 cooled double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.32 Å / Num. all: 173572 / Num. obs: 173572 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.3 % / Net I/σ(I): 14.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 25.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 28468 / % possible all: 100

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.383 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 1737 1 %RANDOM
Rwork0.18151 ---
all0.18181 171834 --
obs0.18181 171834 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9008 0 154 1135 10297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.029461
X-RAY DIFFRACTIONr_bond_other_d0.0010.026373
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.96612887
X-RAY DIFFRACTIONr_angle_other_deg1.101315525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89751157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87824.501451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.698151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4371554
X-RAY DIFFRACTIONr_chiral_restr0.1840.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02110475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021909
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 112 -
Rwork0.339 11806 -
obs--99.99 %
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)
10.1485-0.10580.10570.2374-0.0990.10940.01380.0045-0.0194-0.0137-0.00680.01780.02570.0124-0.0070.0342-0.00120.00220.036-0.00170.00463.91019.8958-24.5007
20.56120.1773-0.13280.3895-0.09640.3402-0.0010.0088-0.0069-0.02070.00610.0406-0.0087-0.0184-0.00510.07450.007-0.0240.05660.00250.0205-9.877717.8262-33.2014
31.032-0.04220.03040.98790.00631.6858-0.0157-0.0050.12060.03790.0092-0.1574-0.16030.2730.00650.0581-0.0142-0.00480.06630.01260.04710.949927.9552-28.7323
40.94220.78230.15771.18830.07650.39010.02550.0039-0.08290.0116-0.011-0.03060.0385-0.0074-0.01450.06370.01-0.00030.0524-0.00330.0227-27.75142.5192-15.016
50.28520.0874-0.10580.2933-0.12060.34930.01090.01030.0188-0.0071-0.0063-0.0211-0.01410.0291-0.00450.05110.002-0.00620.0407-0.00060.0116-1.93625.4726-23.1704
60.3069-0.1094-0.21380.30840.04990.25010.01130.0493-0.0304-0.0448-0.02250.0112-0.004-0.02910.01120.05180.0032-0.02530.0466-0.01220.0236-4.5626-11.9607-24.7812
70.54720.11830.16070.47380.10370.3776-0.00210.0448-0.0567-0.0586-0.0113-0.00260.03860.03870.01340.06690.00910.01240.0449-0.01750.022913.4801-20.3439-30.8695
81.2113-0.12640.38721.00050.02491.63040.01740.0111-0.1636-0.0631-0.0030.3210.1503-0.1883-0.01440.0378-0.0131-0.02930.0459-0.02610.139-12.214-27.5192-30.8108
90.89320.6438-0.19611.1742-0.08030.44040.0184-0.01170.08110.0054-0.01560.0198-0.05440.0287-0.00280.06840.0048-0.00550.0640.00310.017227.7295-3.7615-13.7383
100.41340.06190.12020.41780.09850.3750.00450.0375-0.0919-0.05170.00120.06340.0289-0.0153-0.00570.0477-0.0012-0.00640.0241-0.01410.03662.1062-27.2001-21.6448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 173
2X-RAY DIFFRACTION2A174 - 308
3X-RAY DIFFRACTION3A309 - 358
4X-RAY DIFFRACTION4A359 - 474
5X-RAY DIFFRACTION5A475 - 618
6X-RAY DIFFRACTION6B43 - 169
7X-RAY DIFFRACTION7B170 - 293
8X-RAY DIFFRACTION8B294 - 358
9X-RAY DIFFRACTION9B359 - 471
10X-RAY DIFFRACTION10B472 - 618

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