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- PDB-2c76: Functional Role of the Aromatic Cage in Human Monoamine Oxidase B... -

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Basic information

Entry
Database: PDB / ID: 2c76
TitleFunctional Role of the Aromatic Cage in Human Monoamine Oxidase B: Structures and Catalytic Properties of Tyr435 Mutant Proteins
ComponentsAMINE OXIDASE (FLAVIN-CONTAINING) B
KeywordsOXIDOREDUCTASE / ENANTIOSELECTIVITY / FAD / FLAVIN / FLAVOPROTEIN / HUMAN MONOAMINE OXIDASE / INHIBITOR BINDING / MITOCHONDRION / RASAGILINE / TRANSMEMBRANE / PARKINSON / ACETYLATION
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / dopamine catabolic process / 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 ...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 / N-PROPARGYL-1(S)-AMINOINDAN / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, M. / Binda, C. / Mattevi, A. / Edmondson, D.E.
CitationJournal: Biochemistry / Year: 2006
Title: Functional Role of the Aromatic Cage in Human Monoamine Oxidase B: Structures and Catalytic Properties of Tyr435 Mutant Proteins
Authors: Li, M. / Binda, C. / Mattevi, A. / Edmondson, D.E.
History
DepositionNov 17, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2006Provider: 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_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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)119,6356
Polymers117,7222
Non-polymers1,9144
Water16,394910
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.242, 223.063, 86.361
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-2011-

HOH

21B-2034-

HOH

31B-2372-

HOH

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
12ILEILETHRTHRAA110 - 202110 - 202
22ILEILETHRTHRBB110 - 202110 - 202
13GLYGLYILEILEAA204 - 317204 - 317
23GLYGLYILEILEBB204 - 317204 - 317
14GLYGLYILEILEAA319 - 496319 - 496
24GLYGLYILEILEBB319 - 496319 - 496
15FADFADFADFADAC600
25FADFADFADFADBE600
16RSARSARSARSAAD601
26RSARSARSARSABF601

NCS oper: (Code: given
Matrix: (-0.5272, -0.4976, -0.6888), (-0.4964, -0.4775, 0.725), (-0.6896, 0.7241, 0.0048)
Vector: 139.9176, 208.2615, -54.25)

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Components

#1: Protein AMINE OXIDASE (FLAVIN-CONTAINING) B / MONOAMINE OXIDASE B / MAO-B


Mass: 58860.770 Da / Num. of mol.: 2 / Mutation: YES
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-RSA / N-PROPARGYL-1(S)-AMINOINDAN


Mass: 171.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 434 TO TRP ENGINEERED RESIDUE IN CHAIN B, TYR 434 TO TRP THE ...ENGINEERED RESIDUE IN CHAIN A, TYR 434 TO TRP ENGINEERED RESIDUE IN CHAIN B, TYR 434 TO TRP THE MUTATED RESIDUE IS NUMBERED 435 IN THE COORDINATE RECORDS BELOW.
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: 2.52 Å3/Da / Density % sol: 50.8 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 136583 / % possible obs: 98.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10

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Processing

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

1s2q


Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.91 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3485 2.6 %RANDOM
Rwork0.191 ---
obs0.191 132929 98.5 %-
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: 17.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.2 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7915 0 132 910 8957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228261
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.98411227
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4355991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28123.52358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.491151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6861558
X-RAY DIFFRACTIONr_chiral_restr0.0740.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026206
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.24312
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25693
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2826
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.55091
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89928010
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46533681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.424.53217
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: 3910 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.040.05
tight thermal0.110.5
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 268
Rwork0.269 9756

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