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- PDB-1oja: HUMAN MONOAMINE OXIDASE B IN COMPLEX WITH ISATIN -

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Basic information

Entry
Database: PDB / ID: 1oja
TitleHUMAN MONOAMINE OXIDASE B IN COMPLEX WITH ISATIN
ComponentsAMINE OXIDASE [FLAVIN-CONTAINING] B
KeywordsOXIDOREDUCTASE / FAD-CONTAINING AMINE OXIDASE / FLAVOPROTEIN
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion / : / dopamine catabolic process / primary-amine oxidase / mitochondrial envelope / hydrogen peroxide biosynthetic process / response to corticosterone / substantia nigra development / response to toxic substance / flavin adenine dinucleotide binding / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / electron transfer activity / response to xenobiotic stimulus / neuronal cell body / dendrite / mitochondrion / identical protein binding
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / ISATIN / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsBinda, C. / Edmondson, D.E. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Insights Into the Mode of Inhibition of Human Mitochondrial Monoamine Oxidase B from High-Resolution Crystal Structures
Authors: Binda, C. / Li, M. / Hubalek, F. / Restelli, N. / Edmondson, D.E. / Mattevi, A.
History
DepositionJul 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMINE OXIDASE [FLAVIN-CONTAINING] B
B: AMINE OXIDASE [FLAVIN-CONTAINING] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5416
Polymers117,6752
Non-polymers1,8654
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)130.340, 221.964, 85.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-2028-

HOH

21B-2218-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.53055, -0.49588, -0.68748), (-0.49673, -0.47531, 0.72618), (-0.68686, 0.72677, 0.00586)
Vector: 138.91261, 206.72032, -54.42005)

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Components

#1: Protein AMINE OXIDASE [FLAVIN-CONTAINING] B / MONOAMINE OXIDASE / MAO-B


Mass: 58837.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P27338, monoamine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ISN / ISATIN / Isatin


Mass: 147.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2

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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: 2.85 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %(w/v)PEG40001reservoir
270 mMlithium sulfate1reservoir
3100 mMADA1reservoirpH6.5
42 mg/mlprotein1reservoir
58.5 mMZwittergent3-121reservoir
625 mMpotassium phosphate1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 128815 / % possible obs: 94.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.1 / % possible all: 76.7
Reflection
*PLUS
Highest resolution: 1.7 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 76.7 % / Rmerge(I) obs: 0.339

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.7→15 Å / SU B: 1.764 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.20444 3301 2.6 %RANDOM
Rwork0.1815 ---
obs0.18209 125285 95.04 %-
Displacement parametersBiso mean: 12.139 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.58 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 128 660 8699
Refinement
*PLUS
Highest resolution: 1.7 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.4

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