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- PDB-2byb: Human Monoamine Oxidase B in complex with Deprenyl -

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Basic information

Entry
Database: PDB / ID: 2byb
TitleHuman Monoamine Oxidase B in complex with Deprenyl
ComponentsAMINE OXIDASE [FLAVIN-CONTAINING] B
KeywordsOXIDOREDUCTASE / FAD-CONTAINING AMINE OXIDASE / MAOB ACETYLATION / FAD / FLAVOPROTEIN / MAOB / TRANSMEMBRANE NEUROTRANSMITTER / MEMBRANE-PROTEIN
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / substantia nigra development / flavin adenine dinucleotide binding ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / substantia nigra development / flavin adenine dinucleotide binding / mitochondrial outer membrane / electron transfer activity / mitochondrion
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 ...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
DEPRENYL / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBinda, C. / De Colibus, L. / Edmondson, D.E. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Three-Dimensional Structure of Human Monoamine Oxidase a (Mao A): Relation to the Structures of Rat Mao a and Human Mao B
Authors: De Colibus, L. / Li, M. / Binda, C. / Lustig, A. / Edmondson, D.E. / Mattevi, A.
History
DepositionJul 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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_conn / struct_ncs_dom_lim / 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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)119,6256
Polymers117,6752
Non-polymers1,9504
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-16.2 kcal/mol
Surface area44850 Å2
MethodPQS
Unit cell
Length a, b, c (Å)132.835, 225.840, 85.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPHEPHEAA3 - 993 - 99
21ASNASNPHEPHEBB3 - 993 - 99
12ILEILEILEILEAA110 - 496110 - 496
22ILEILEILEILEBB110 - 496110 - 496
13FADFADFADFADAC600
23FADFADFADFADBE600
14DPKDPKDPKDPKAD601
24DPKDPKDPKDPKBF601

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Components

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DPK / DEPRENYL / N-METHYL-N-[(1R)-1-METHYL-2-PHENYLETHYL]PROP-2-EN-1-AMINE


Mass: 189.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.73 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.2 / Details: pH 6.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 60540 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S2Q

1s2q


Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.865 / SU B: 14.752 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1605 2.6 %RANDOM
Rwork0.237 ---
obs0.239 60540 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å20 Å20 Å2
2--5.17 Å20 Å2
3----2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 134 489 8534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228253
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.98611213
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13123.52358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.666151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5611558
X-RAY DIFFRACTIONr_chiral_restr0.1090.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026204
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.23928
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25557
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2598
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5420.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7961.55080
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20528008
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17333684
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.954.53205
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3924 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.080.05
tight thermal0.220.5
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.442 118
Rwork0.356 4491
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71340.0694-0.18390.69720.11510.4353-0.1270.1107-0.0406-0.07120.1217-0.15680.02450.02360.0052-0.0518-0.08330.0051-0.0763-0.0702-0.027253.2683149.318824.2324
20.77280.2328-0.07250.6226-0.08530.5343-0.12280.2384-0.0303-0.09370.15110.01740.02040.0221-0.0283-0.0327-0.12060.0089-0.0834-0.0791-0.050822.1056130.646315.9274
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 501
2X-RAY DIFFRACTION2B3 - 496

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