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- PDB-8eek: C. ammoniagenes monoamine oxidase (MAO) bound to tyramine -

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Basic information

Entry
Database: PDB / ID: 8eek
TitleC. ammoniagenes monoamine oxidase (MAO) bound to tyramine
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / Monoamine / oxidase / flavoenzyme / substrate
Function / homologyAmine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / 4-(2-aminoethyl)phenol / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase
Function and homology information
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsMuellers, S.N. / Allen, K.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2023
Title: Structural Insights into the Substrate Range of a Bacterial Monoamine Oxidase.
Authors: Muellers, S.N. / Tararina, M.A. / Kuzmanovic, U. / Galagan, J.E. / Allen, K.N.
History
DepositionSep 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amine oxidase
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8906
Polymers100,0452
Non-polymers1,8454
Water9,746541
1
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9453
Polymers50,0221
Non-polymers9232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9453
Polymers50,0221
Non-polymers9232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.881, 118.600, 141.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Amine oxidase


Mass: 50022.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium ammoniagenes (bacteria)
Gene: CA40472_00570 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A807MR40
#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-AEF / 4-(2-aminoethyl)phenol


Mass: 137.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 10 - 15% w/v PEG-3350, 0.1 M sodium malonate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.51→38.07 Å / Num. obs: 157374 / % possible obs: 99.2 % / Redundancy: 25.8 % / Biso Wilson estimate: 16.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.272 / Rpim(I) all: 0.054 / Rrim(I) all: 0.278 / Net I/σ(I): 15
Reflection shellResolution: 1.51→1.564 Å / Redundancy: 25.2 % / Rmerge(I) obs: 1.371 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 15566 / CC1/2: 0.643 / Rpim(I) all: 0.489 / % possible all: 99.34

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→38.07 Å / SU ML: 0.176 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.828
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.239 1266 0.81 %
Rwork0.228 --
obs0.228 156967 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.26 Å2
Refinement stepCycle: LAST / Resolution: 1.51→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6798 0 126 541 7465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097098
X-RAY DIFFRACTIONf_angle_d1.0369671
X-RAY DIFFRACTIONf_dihedral_angle_d17.4442457
X-RAY DIFFRACTIONf_chiral_restr0.0731035
X-RAY DIFFRACTIONf_plane_restr0.0061237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.570.33681390.307117128X-RAY DIFFRACTION99
1.57-1.640.28821390.284717074X-RAY DIFFRACTION99
1.64-1.730.25441400.263417184X-RAY DIFFRACTION99
1.73-1.840.28581400.248617235X-RAY DIFFRACTION100
1.84-1.980.26151390.238817170X-RAY DIFFRACTION99
1.98-2.180.27181410.229317362X-RAY DIFFRACTION100
2.18-2.490.22621410.228817289X-RAY DIFFRACTION99
2.49-3.140.24161420.231917407X-RAY DIFFRACTION99
3.14-38.070.20351450.198917852X-RAY DIFFRACTION99

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