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- PDB-1w1k: STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: ... -

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Basic information

Entry
Database: PDB / ID: 1w1k
TitleSTRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Ile238Thr Mutant
ComponentsVANILLYL-ALCOHOL OXIDASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / CATALYSIS / FAD
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / methanol metabolic process / lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / D-lactate dehydrogenase (NAD+) activity / FAD binding / peroxisome / mitochondrion
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / 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 / FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / 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
2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol / FLAVIN-ADENINE DINUCLEOTIDE / Vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesPENICILLIUM SIMPLICISSIMUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsVan Den Heuvel, R.H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Laboratory-Evolved Vanillyl-Alcohol Oxidase Produces Natural Vanillin
Authors: Van Den Heuvel, R.H. / Van Den Berg, W.A. / Rovida, S. / Van Berkel, W.J.
History
DepositionJun 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0906
Polymers126,1902
Non-polymers1,9004
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.896, 129.896, 133.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein VANILLYL-ALCOHOL OXIDASE / ARYL-ALCOHOL OXIDASE / 4-ALLYLPHENOL OXIDASE


Mass: 63095.066 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COVALENT BOND BETWEEN FAD AND HIS 422 / Source: (gene. exp.) PENICILLIUM SIMPLICISSIMUM (fungus) / Description: FUNGUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P56216, alcohol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EUG / 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol / Isoeugenol


Mass: 164.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O2
Compound detailsENGINEERED RESIDUES CHAINS A, B : ILE (238) THR
Has protein modificationY

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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: 40 % / Description: BINDING STUDIES
Crystal growpH: 4.6 / Details: FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 33857 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VAO

2vao


Resolution: 2.55→40 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.381 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1778 5 %RANDOM
Rwork0.207 ---
obs0.21 33857 98.9 %-
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: 46.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å20 Å2
2---1.88 Å20 Å2
3---3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8700 0 128 0 8828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0219079
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.96512354
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99351096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026934
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.24302
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5611.55472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05828848
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66533606
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6284.53506
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 119
Rwork0.282 2461

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