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- PDB-8eeh: C. ammoniagenes monoamine oxidase (MAO) bound to tryptamine -

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Basic information

Entry
Database: PDB / ID: 8eeh
TitleC. ammoniagenes monoamine oxidase (MAO) bound to tryptamine
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / Monoamine / oxidase / substrate / flavoenzyme
Function / homologyAmine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / 2-(1H-INDOL-3-YL)ETHANAMINE / Amine oxidase
Function and homology information
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 1.2Mar 13, 2024Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen

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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)101,9366
Polymers100,0452
Non-polymers1,8924
Water5,278293
1
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9683
Polymers50,0221
Non-polymers9462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9683
Polymers50,0221
Non-polymers9462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.989, 97.868, 141.607
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-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H12N2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
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: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.78→38.87 Å / Num. obs: 85341 / % possible obs: 99.26 % / Redundancy: 5.8 % / Biso Wilson estimate: 20.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.028 / Rrim(I) all: 0.07 / Net I/σ(I): 15.6
Reflection shellResolution: 1.78→1.844 Å / Redundancy: 3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8024 / CC1/2: 0.645 / Rpim(I) all: 0.572 / Rrim(I) all: 1.056 / % possible all: 94.4

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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: 1.78→38.87 Å / SU ML: 0.249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.703
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.248 1545 1.81 %
Rwork0.214 --
obs0.215 85257 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.23 Å2
Refinement stepCycle: LAST / Resolution: 1.78→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6812 0 130 293 7235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087120
X-RAY DIFFRACTIONf_angle_d0.9659702
X-RAY DIFFRACTIONf_dihedral_angle_d19.5692464
X-RAY DIFFRACTIONf_chiral_restr0.0581035
X-RAY DIFFRACTIONf_plane_restr0.0051240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.840.35181330.32197105X-RAY DIFFRACTION94
1.84-1.90.33051360.27027432X-RAY DIFFRACTION98
1.9-1.980.29671400.23857577X-RAY DIFFRACTION100
1.98-2.070.26391400.22847581X-RAY DIFFRACTION100
2.07-2.180.27281400.22937588X-RAY DIFFRACTION100
2.18-2.310.26461400.21987610X-RAY DIFFRACTION100
2.31-2.490.28941420.22587651X-RAY DIFFRACTION100
2.49-2.740.29281400.22297657X-RAY DIFFRACTION100
2.74-3.140.24381420.227702X-RAY DIFFRACTION100
3.14-3.960.22821430.19827766X-RAY DIFFRACTION100
3.96-38.870.18271490.18168043X-RAY DIFFRACTION100

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