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- PDB-8eej: C. ammoniagenes monoamine oxidase (MAO) C424S variant bound to do... -

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Basic information

Entry
Database: PDB / ID: 8eej
TitleC. ammoniagenes monoamine oxidase (MAO) C424S variant bound to dopamine
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / Flavoenzyme / substrate
Function / homologyAmine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / L-DOPAMINE / Amine oxidase
Function and homology information
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,8906
Polymers100,0132
Non-polymers1,8774
Water11,584643
1
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9453
Polymers50,0061
Non-polymers9392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9453
Polymers50,0061
Non-polymers9392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.207, 117.861, 141.032
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: 50006.410 Da / Num. of mol.: 2 / Mutation: C424S
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-LDP / L-DOPAMINE / DOPAMINE


Mass: 153.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#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.: 643 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
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-1 / Wavelength: 0.977 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.54→29.82 Å / Num. obs: 147936 / % possible obs: 99.71 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Net I/σ(I): 11.4
Reflection shellResolution: 1.54→1.596 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 14311 / CC1/2: 0.762 / Rpim(I) all: 0.303 / Rrim(I) all: 0.737 / % possible all: 97.59

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EEI

8eei


Resolution: 1.54→29.82 Å / SU ML: 0.1497 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 2000 1.35 %
Rwork0.1832 145932 -
obs0.1834 147932 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.02 Å2
Refinement stepCycle: LAST / Resolution: 1.54→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6886 0 128 643 7657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00867226
X-RAY DIFFRACTIONf_angle_d1.01629852
X-RAY DIFFRACTIONf_chiral_restr0.06061048
X-RAY DIFFRACTIONf_plane_restr0.00531264
X-RAY DIFFRACTIONf_dihedral_angle_d19.23792504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.27161370.227610002X-RAY DIFFRACTION96.64
1.58-1.620.26541420.218410310X-RAY DIFFRACTION99.96
1.62-1.670.24141410.212810370X-RAY DIFFRACTION100
1.67-1.720.26511420.2110348X-RAY DIFFRACTION99.99
1.72-1.790.21951420.195610374X-RAY DIFFRACTION100
1.79-1.860.23681430.200110347X-RAY DIFFRACTION99.98
1.86-1.940.20131420.186110418X-RAY DIFFRACTION99.98
1.94-2.040.20531420.184710358X-RAY DIFFRACTION99.98
2.04-2.170.20911430.183810419X-RAY DIFFRACTION99.99
2.17-2.340.20491430.181210450X-RAY DIFFRACTION99.98
2.34-2.580.18441430.18310466X-RAY DIFFRACTION99.99
2.58-2.950.21561450.188610514X-RAY DIFFRACTION99.92
2.95-3.710.17571450.178710608X-RAY DIFFRACTION99.93
3.71-29.820.15081500.157110948X-RAY DIFFRACTION99.93

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