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- PDB-3fim: Crystal structure of aryl-alcohol-oxidase from Pleurotus eryingii -

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Basic information

Entry
Database: PDB / ID: 3fim
TitleCrystal structure of aryl-alcohol-oxidase from Pleurotus eryingii
ComponentsAryl-alcohol oxidase
KeywordsOXIDOREDUCTASE / AAO / lignin degradation / Pleurotus eryngii / Flavoprotein
Function / homology
Function and homology information


aryl-alcohol oxidase / aryl-alcohol oxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / flavin adenine dinucleotide binding
Similarity search - Function
Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Aryl-alcohol oxidase
Similarity search - Component
Biological speciesPleurotus eryngii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsFernandez, I.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Novel structural features in the GMC family of oxidoreductases revealed by the crystal structure of fungal aryl-alcohol oxidase
Authors: Fernandez, I.S. / Ruiz-Duenas, F.J. / Santillana, E. / Ferreira, P. / Martinez, M.J. / Martinez, A.T. / Romero, A.
History
DepositionDec 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Aryl-alcohol oxidase
B: FLAVIN-ADENINE DINUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7592
Polymers60,9741
Non-polymers7861
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)180.226, 180.226, 160.407
Angle α, β, γ (deg.)90.00, 90.00, 120
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Aryl-alcohol oxidase /


Mass: 60973.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus eryngii (fungus) / Gene: aao / Plasmid: pFLAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: O94219, aryl-alcohol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2

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Sample preparation

CrystalDensity Matthews: 6.17 Å3/Da / Density % sol: 80.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1M lithium sulfate, 0.1M Bis-Tris propane, pH7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1610.85
SYNCHROTRONEMBL/DESY, Hamburg BW7A20.978
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 23, 2003
MARRESEARCH2CCDJan 18, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.851
20.9781
ReflectionResolution: 2.39→37.7 Å / Num. obs: 56141 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 15 % / Biso Wilson estimate: 35.68 Å2 / Rmerge(I) obs: 0.102
Reflection shellResolution: 2.39→37.7 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4 / % possible all: 88.8

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Processing

Software
NameVersionClassification
SHELXSphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.55→20.04 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.365 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 2995 5.1 %RANDOM
Rwork0.17336 ---
obs0.17507 49123 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.55→20.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 53 225 4574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0224464
X-RAY DIFFRACTIONr_angle_refined_deg2.6931.9616117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12124.577201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25215644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5081525
X-RAY DIFFRACTIONr_chiral_restr0.2620.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023492
X-RAY DIFFRACTIONr_nbd_refined0.2170.21842
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2206
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.25
X-RAY DIFFRACTIONr_mcbond_it1.4171.52956
X-RAY DIFFRACTIONr_mcangle_it2.18324565
X-RAY DIFFRACTIONr_scbond_it3.80431829
X-RAY DIFFRACTIONr_scangle_it5.3354.51552
LS refinement shellResolution: 2.392→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 172 -
Rwork0.236 3783 -
obs--89.3 %
Refinement TLS params.Method: refined / Origin x: -21.244 Å / Origin y: 67.828 Å / Origin z: -10.402 Å
111213212223313233
T-0.1767 Å2-0.0225 Å2-0.0593 Å2-0.0053 Å2-0.0036 Å2---0.155 Å2
L1.5361 °20.1731 °20.0986 °2-0.8837 °2-0.0883 °2--0.8675 °2
S-0.0157 Å °-0.096 Å °0.0558 Å °0.0075 Å °-0.0384 Å °0.0107 Å °0.0653 Å °-0.0075 Å °0.0541 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B0
2X-RAY DIFFRACTION1B2 - 566

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