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- PDB-4mok: Pyranose 2-oxidase H167A mutant soaked with 3-fluorinated galacto... -

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Basic information

Entry
Database: PDB / ID: 4mok
TitlePyranose 2-oxidase H167A mutant soaked with 3-fluorinated galactose (not bound)
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / GMC OXIDOREDUCTASE / PHBH FOLD / HOMOTETRAMER / FAD-BINDING / 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
FLAVIN-ADENINE DINUCLEOTIDE / 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 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Pyranose 2-oxidase
D: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,66714
Polymers281,9484
Non-polymers5,71910
Water32,3011793
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25180 Å2
ΔGint-133 kcal/mol
Surface area79940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.875, 102.295, 136.957
Angle α, β, γ (deg.)90.00, 90.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyranose 2-oxidase / Pyranose oxidase


Mass: 70486.984 Da / Num. of mol.: 4 / Mutation: H167A
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1793 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
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: Diamond / Beamline: I24 / Wavelength: 0.9191 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2013
Details: Oxford Danfysik/SESO two stage demagnification using two K-B pairs of bimorph type mirrors
RadiationMonochromator: ACCEL fixed-exit double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 1.9→47.92 Å / Num. all: 216233 / Num. obs: 216233 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 30699 / % possible all: 99.8

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.92 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.626 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21382 1066 0.5 %RANDOM
Rwork0.17015 ---
obs0.17037 215167 99.83 %-
all-215167 --
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: 32.707 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å2-0.25 Å2
2---0.26 Å20 Å2
3---2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18089 0 297 1793 20179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0218861
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212723
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.96525634
X-RAY DIFFRACTIONr_angle_other_deg0.959331001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13552293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30624.502893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.493153018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0215108
X-RAY DIFFRACTIONr_chiral_restr0.1480.22788
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02120868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023790
LS refinement shellResolution: 1.9→2.003 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.269 169 -
Rwork0.267 30664 -
obs--99.8 %
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)
10.39480.0089-0.04170.36960.02430.313-0.00070.0468-0.0576-0.04360.01270.0360.017-0.0096-0.0120.08430.0041-0.00660.0669-0.00440.0621-21.909118.06-65.7037
20.94930.79690.07481.53750.29760.56380.0229-0.05010.12310.01470.01230.0642-0.02330.0523-0.03520.10160.02350.00470.1035-0.00430.0715-0.099327.3094-52.7817
30.47370.11460.18940.40650.20270.50220.0290.003-0.0889-0.0070.00030.05510.0547-0.0269-0.02930.06620.0021-0.00140.0461-0.00270.0539-19.35689.5663-58.5467
40.3838-0.10430.13830.4499-0.13970.40830.00920.0006-0.0026-0.02450.04080.11680.0128-0.0428-0.050.0619-0.00040.00280.05050.02020.0773-31.440247.7985-59.9498
52.05360.94250.60942.7430.26181.5583-0.0322-0.0139-0.25010.05450.0899-0.18110.13410.09-0.05770.04060.00850.01950.09820.05520.1218-41.298545.8639-49.8691
60.44940.0331-0.09880.4819-0.28520.5318-0.0028-0.00220.07370.01480.03570.036-0.0559-0.0025-0.03280.04960.00760.01250.03040.0090.0692-27.93557.8511-54.3791
70.3071-0.0560.08720.4332-0.11370.57590.0157-0.0465-0.02590.12760.0238-0.0015-0.00010.0011-0.03950.14910.00270.00010.10390.00660.0061-5.277627.2301-9.5899
82.03680.5261-0.1311.5972-0.10840.65930.0081-0.17750.12510.1340.06120.27540.1115-0.0837-0.06930.1657-0.0002-0.0010.09520.03320.0603-15.52664.4769-20.6422
90.17420.10680.19110.39110.08890.71350.0017-0.03350.00940.10150.0216-0.0626-0.06950.0846-0.02330.11140.0048-0.02130.0745-0.01420.01993.13228.7639-15.5333
100.5203-0.09050.14070.4521-0.07130.48880.0042-0.2797-0.08770.20340.07460.1731-0.0472-0.1769-0.07880.1060.02460.08240.18260.07190.0806-37.5532.6051-7.4364
112.38341.29470.58161.78290.08490.5878-0.1027-0.2836-0.14280.25560.0686-0.0944-0.1364-0.07160.03410.19130.05970.0430.1258-0.01030.058-27.048758.2292-15.8321
120.55860.11790.08270.5343-0.26330.7108-0.0253-0.2659-0.11160.14990.11380.21840.0004-0.2553-0.08850.06420.04390.08940.20950.11910.1435-46.268632.4093-13.0453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 341
2X-RAY DIFFRACTION2A342 - 461
3X-RAY DIFFRACTION3A462 - 618
4X-RAY DIFFRACTION4B44 - 427
5X-RAY DIFFRACTION5B428 - 460
6X-RAY DIFFRACTION6B461 - 618
7X-RAY DIFFRACTION7C45 - 392
8X-RAY DIFFRACTION8C393 - 461
9X-RAY DIFFRACTION9C462 - 618
10X-RAY DIFFRACTION10D46 - 388
11X-RAY DIFFRACTION11D389 - 461
12X-RAY DIFFRACTION12D462 - 617

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