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- PDB-1e8h: STRUCTURE OF THE H61T MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL ... -

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Basic information

Entry
Database: PDB / ID: 1e8h
TitleSTRUCTURE OF THE H61T MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN THE APO FORM COMPLEXED BY ADP
ComponentsVANILLYL-ALCOHOL OXIDASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / METHANOL UTILIZATION / PEROXISOME / FLAVOENZYME / 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
ADENOSINE-5'-DIPHOSPHATE / Vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesPENICILLIUM SIMPLICISSIMUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMattevi, A. / Fraaije, M.W.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structural Analysis of Flavinylation in Vanillyl-Alcohol Oxidase
Authors: Fraaije, M.W. / Van Der Heuvel, R.H.H. / Van Berkel, W.J.H. / Mattevi, A.
History
DepositionSep 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2000Provider: 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_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

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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)126,7944
Polymers125,9402
Non-polymers8542
Water1,60389
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)507,17716
Polymers503,7598
Non-polymers3,4188
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
Buried area50950 Å2
ΔGint-376.5 kcal/mol
Surface area176870 Å2
MethodPQS
Unit cell
Length a, b, c (Å)130.340, 130.340, 134.000
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: (0.238137, -0.971199, 0.007873), (-0.97113, -0.238222, -0.012497), (0.014012, -0.004669, -0.999891)
Vector: 112.601, 144.819, 110.844)
DetailsBIOLOGICAL_UNIT: HOMOOCTAMER

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Components

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


Mass: 62969.934 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PENICILLIUM SIMPLICISSIMUM (fungus) / Description: FUNGUS / Cellular location: INTRACELLULAR / Organelle: PEROXISOMES / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P56216, aryl-alcohol oxidase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE CONVERSION OF VANILLIN ALCOHOL TO VANILLIN, AND A WIDE RANGE OF PHENOLIC COMPOUNDS OF ...CATALYZES THE CONVERSION OF VANILLIN ALCOHOL TO VANILLIN, AND A WIDE RANGE OF PHENOLIC COMPOUNDS OF VARIABLE SIZE SIDE CHAIN AT THE PARA POSITION. CRUCIAL IN THE DEGRADATION OF THE SECONDARY METABOLITES RESULTING FROM THE DEGRADATION OF THE LIGNIN.

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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: 45.56 %
Crystal growpH: 4.6 / Details: FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Crystal grow
*PLUS
pH: 5.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 %(w/v)PEG40001reservoir
2100 mMsodium acetate/HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 34320 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.393 / % possible all: 100
Reflection
*PLUS
Num. measured all: 85638
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

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

1qlt


Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1000 3 %RANDOM
Rwork0.237 ---
obs0.237 34320 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8622 0 54 89 8765
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.020.04
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
Type: p_plane_restr / Dev ideal: 0.01

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