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- PDB-2vao: STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE I... -

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Basic information

Entry
Database: PDB / ID: 2vao
TitleSTRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH ISOEUGENOL
ComponentsVANILLYL-ALCOHOL OXIDASE
KeywordsFLAVOENZYME / OXIDASE / CATALYSIS
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 / DENSITY AVERAGING, LEAST SQUARES REFINEMENT / Resolution: 2.8 Å
AuthorsMattevi, A.
CitationJournal: Structure / Year: 1997
Title: Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity.
Authors: Mattevi, A. / Fraaije, M.W. / Mozzarelli, A. / Olivi, L. / Coda, A. / van Berkel, W.J.
History
DepositionApr 10, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)128,1146
Polymers126,2142
Non-polymers1,9004
Water68538
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)512,45524
Polymers504,8578
Non-polymers7,59816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)128.380, 128.380, 130.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.23341, -0.97158, 0.03932), (-0.97189, -0.23438, -0.02231), (0.03089, -0.033, -0.99898)
Vector: 109.69416, 143.16341, 110.29491)

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Components

#1: Protein VANILLYL-ALCOHOL OXIDASE


Mass: 63107.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FUNGUS / Source: (natural) Penicillium simplicissimum (fungus) / Cellular location: INTRACELLULAR / Organelle: PEROXISOMES / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
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
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %(w/v)PEG40001reservoir
20.1 Msodium acetate/HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 23480 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.112 / Net I/σ(I): 8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3 / Rsym value: 0.322 / % possible all: 83.1
Reflection
*PLUS
Num. measured all: 175968 / Rmerge(I) obs: 0.118
Reflection shell
*PLUS
% possible obs: 83.1 %

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Processing

Software
NameVersionClassification
CCP4model building
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: DENSITY AVERAGING, LEAST SQUARES REFINEMENT
Resolution: 2.8→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rfree0.29 1000 3 %
Rwork0.214 --
all0.215 23480 -
obs0.215 23480 90.6 %
Solvent computationSolvent model: BABINET
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8782 0 128 38 8948
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.017916030
X-RAY DIFFRACTIONt_angle_deg3.81239615
X-RAY DIFFRACTIONt_dihedral_angle_d21.1295296180
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011214100
X-RAY DIFFRACTIONt_gen_planes0.0091312250
X-RAY DIFFRACTIONt_it7915665
X-RAY DIFFRACTIONt_nbd0.064616125
Software
*PLUS
Name: TNT / Version: 5-E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.295
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg21.129180
X-RAY DIFFRACTIONt_planar_d0.011100
X-RAY DIFFRACTIONt_plane_restr0.009250

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