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- PDB-1e0y: Structure of the D170S/T457E double mutant of vanillyl-alcohol oxidase -

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Basic information

Entry
Database: PDB / ID: 1e0y
TitleStructure of the D170S/T457E double mutant of vanillyl-alcohol oxidase
ComponentsVANILLYL-ALCOHOL OXIDASE
KeywordsFLAVOENZYME / SPECIFICITY
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
FLAVIN-ADENINE DINUCLEOTIDE / ALPHA,ALPHA,ALPHA-TRIFLUORO-P-CRESOL / Vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesPENICILLIUM SIMPLICISSIMUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsVan Der heuvel, R.H.H. / Van Berkel, W.J.H. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Inversion of Stereospecificity in Vanillyl-Alcohol Oxidase
Authors: Van Der Heuvel, R.H.H. / Fraaije, M.W. / Espinosa, M.F. / Mattevi, A. / Van Berkel, W.J.H.
History
DepositionApr 11, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)127,7475
Polymers126,0142
Non-polymers1,7333
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.281, 131.281, 134.355
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 / VAO


Mass: 63006.980 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN FLAVIN AND HIS422 / Source: (gene. exp.) PENICILLIUM SIMPLICISSIMUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG2 / References: UniProt: P56216, vanillyl-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-FCR / ALPHA,ALPHA,ALPHA-TRIFLUORO-P-CRESOL


Mass: 162.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5F3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION ASP170SER AND THR457GLU
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: 46.45 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMpotassium phosphate1drop
3100 mMsodium acetate/hydrochloride1reservoir
43 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 28714 / % possible obs: 97.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 6.4
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.307 / % possible all: 95
Reflection
*PLUS
Num. measured all: 69063
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VAO

1vao


Resolution: 2.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 -2 %RANDOM
Rwork0.225 ---
obs0.225 28714 97.3 %-
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8556 0 117 80 8753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_planar_d0.019
X-RAY DIFFRACTIONp_plane_restr0.001

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