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- PDB-5mxu: Structure of the Y503F mutant of vanillyl alcohol oxidase -

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Basic information

Entry
Database: PDB / ID: 5mxu
TitleStructure of the Y503F mutant of vanillyl alcohol oxidase
ComponentsVanillyl-alcohol oxidase
KeywordsOXIDOREDUCTASE / vanillyl alcohol oxidase / Y503F mutant
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / methanol metabolic process / FAD binding / peroxisome
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 ...Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesPenicillium simplicissimum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEwing, T.A. / Nguyen, Q.-T. / Allan, R.C. / Gygli, G. / Romero, E. / Binda, C. / Fraaije, M.W. / Mattevi, A. / van Berkel, W.J.H.
Funding support Netherlands, Italy, 2items
OrganizationGrant numberCountry
European UnionINDOX project (FP7-KBBE-2013-7-613549) Netherlands
European Community Seventh Framework Programme (FP7/2007-2013)BioStruct-X (Grants 7551 and 10205) Italy
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase.
Authors: Ewing, T.A. / Nguyen, Q.T. / Allan, R.C. / Gygli, G. / Romero, E. / Binda, C. / Fraaije, M.W. / Mattevi, A. / van Berkel, W.J.H.
History
DepositionJan 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vanillyl-alcohol oxidase
B: Vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9386
Polymers126,1822
Non-polymers1,7554
Water4,179232
1
A: Vanillyl-alcohol oxidase
B: Vanillyl-alcohol oxidase
hetero molecules

A: Vanillyl-alcohol oxidase
B: Vanillyl-alcohol oxidase
hetero molecules

A: Vanillyl-alcohol oxidase
B: Vanillyl-alcohol oxidase
hetero molecules

A: Vanillyl-alcohol oxidase
B: Vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,75024
Polymers504,7298
Non-polymers7,02116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Unit cell
Length a, b, c (Å)138.012, 138.012, 132.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 999
2114B1 - 999

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.316585, 0.947382, 0.04735), (0.946804, 0.312564, 0.076586), (0.057756, 0.069077, -0.995938)-25.8107, 16.70728, 34.01067

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Components

#1: Protein Vanillyl-alcohol oxidase / / 4-allylphenol oxidase / Aryl-alcohol oxidase


Mass: 63091.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The residues that are not present in the coordinates are disordered and not visible in the electron density. They are not included in the final model. Side chain atoms of residues His149A, ...Details: The residues that are not present in the coordinates are disordered and not visible in the electron density. They are not included in the final model. Side chain atoms of residues His149A, Ser328A, His149B, Ser328B which lie on the protein surface" have been included in the pdb but set at zero occupancy because they completely lack electron density.
Source: (gene. exp.) Penicillium simplicissimum (fungus) / Gene: VAOA / Production host: Escherichia coli (E. coli) / References: UniProt: P56216, vanillyl-alcohol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.8→54.94 Å / Num. all: 65596 / Num. obs: 27846 / % possible obs: 91.8 % / Redundancy: 2.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.087 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 1.3 / Num. unique all: 10160 / Num. unique obs: 4226 / CC1/2: 0.54 / Rpim(I) all: 0.545 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VAO

2vao


Resolution: 2.8→54.94 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.901 / SU B: 18.61 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24886 1353 4.9 %RANDOM
Rwork0.17522 ---
obs0.17884 26493 90.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2--1.55 Å20 Å2
3----3.11 Å2
Refinement stepCycle: 1 / Resolution: 2.8→54.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8706 0 118 232 9056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199059
X-RAY DIFFRACTIONr_bond_other_d0.0020.028222
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9712337
X-RAY DIFFRACTIONr_angle_other_deg1.013319081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18151105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78224.1400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.979151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.341550
X-RAY DIFFRACTIONr_chiral_restr0.0810.21324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110035
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021849
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_it2.8015.2744429
X-RAY DIFFRACTIONr_mcbond_other2.8015.2744428
X-RAY DIFFRACTIONr_mcangle_it4.4977.9075531
X-RAY DIFFRACTIONr_mcangle_other4.4977.9075532
X-RAY DIFFRACTIONr_scbond_it2.6385.5054629
X-RAY DIFFRACTIONr_scbond_other2.6385.5054629
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2628.1536807
X-RAY DIFFRACTIONr_long_range_B_refined6.78261.1410472
X-RAY DIFFRACTIONr_long_range_B_other6.77961.14810467
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 8490 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.330.5
medium thermal6.072
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 83 -
Rwork0.302 2044 -
obs--93.37 %

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