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- PDB-8eef: C. ammoniagenes monoamine oxidase (MAO) bound to octopamine -

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Basic information

Entry
Database: PDB / ID: 8eef
TitleC. ammoniagenes monoamine oxidase (MAO) bound to octopamine
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / Monoamine / oxidase / substrate / flavoenzyme
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 4-(2R-AMINO-1-HYDROXYETHYL)PHENOL / 4-(2S-AMINO-1-HYDROXYETHYL)PHENOL / Amine oxidase
Similarity search - Component
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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)101,9226
Polymers100,0452
Non-polymers1,8774
Water3,855214
1
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9613
Polymers50,0221
Non-polymers9392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9613
Polymers50,0221
Non-polymers9392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.100, 98.691, 143.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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-OTS / 4-(2S-AMINO-1-HYDROXYETHYL)PHENOL / S-OCTOPAMINE


Mass: 153.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-OTR / 4-(2R-AMINO-1-HYDROXYETHYL)PHENOL / R-OCTOPAMINE


Mass: 153.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.21→29.98 Å / Num. obs: 46205 / % possible obs: 99.92 % / Redundancy: 25.6 % / Biso Wilson estimate: 35.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.045 / Rrim(I) all: 0.224 / Net I/σ(I): 13.8
Reflection shellResolution: 2.21→2.289 Å / Redundancy: 24.8 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4531 / CC1/2: 0.933 / Rpim(I) all: 0.183 / Rrim(I) all: 0.916 / % possible all: 99.87

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→29.89 Å / SU ML: 0.2179 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.3053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2395 1729 3.74 %
Rwork0.1964 44470 -
obs0.198 46199 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.12 Å2
Refinement stepCycle: LAST / Resolution: 2.21→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 0 128 214 7138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857094
X-RAY DIFFRACTIONf_angle_d1.09659664
X-RAY DIFFRACTIONf_chiral_restr0.06191035
X-RAY DIFFRACTIONf_plane_restr0.00611235
X-RAY DIFFRACTIONf_dihedral_angle_d20.59752458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.280.26971410.23663625X-RAY DIFFRACTION99.95
2.28-2.350.2751430.21573664X-RAY DIFFRACTION100
2.35-2.430.26381390.21993618X-RAY DIFFRACTION100
2.43-2.530.24051450.21293687X-RAY DIFFRACTION99.97
2.53-2.640.28071410.21463664X-RAY DIFFRACTION100
2.64-2.780.26731440.21643683X-RAY DIFFRACTION99.97
2.78-2.960.26911440.2113685X-RAY DIFFRACTION99.97
2.96-3.190.2591440.21973708X-RAY DIFFRACTION100
3.19-3.510.23661430.19843683X-RAY DIFFRACTION100
3.51-4.010.23881460.18533754X-RAY DIFFRACTION100
4.01-5.050.21181450.15993760X-RAY DIFFRACTION99.97
5.05-29.890.21341540.19543939X-RAY DIFFRACTION100

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