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- PDB-8eel: C. ammoniagenes monoamine oxidase (MAO) bound to 5-aminopentanol -

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Basic information

Entry
Database: PDB / ID: 8eel
TitleC. ammoniagenes monoamine oxidase (MAO) bound to 5-aminopentanol
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 / 5-aminopentan-1-ol / Amine oxidase
Function and homology information
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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)101,8226
Polymers100,0452
Non-polymers1,7774
Water13,133729
1
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9113
Polymers50,0221
Non-polymers8892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9113
Polymers50,0221
Non-polymers8892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.820, 118.541, 141.081
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-WHX / 5-aminopentan-1-ol


Mass: 103.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 50.8 %
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: 1.97→38.05 Å / Num. obs: 70509 / % possible obs: 98.21 % / Redundancy: 25.4 % / Biso Wilson estimate: 19.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.023 / Rrim(I) all: 0.116 / Net I/σ(I): 24.7
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 20 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 5 / Num. unique obs: 6388 / CC1/2: 0.946 / Rpim(I) all: 0.17 / Rrim(I) all: 0.781 / % possible all: 89.86

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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: 1.97→38.05 Å / SU ML: 0.1826 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.212 1473 2.09 %
Rwork0.1781 69009 -
obs0.1788 70482 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.09 Å2
Refinement stepCycle: LAST / Resolution: 1.97→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6880 0 120 729 7729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00767180
X-RAY DIFFRACTIONf_angle_d0.85739781
X-RAY DIFFRACTIONf_chiral_restr0.05641045
X-RAY DIFFRACTIONf_plane_restr0.00511255
X-RAY DIFFRACTIONf_dihedral_angle_d20.40232498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.23221200.19835644X-RAY DIFFRACTION89.45
2.03-2.110.22931330.19046202X-RAY DIFFRACTION98.22
2.11-2.190.20191330.18486269X-RAY DIFFRACTION99.58
2.19-2.290.22431350.18036305X-RAY DIFFRACTION99.54
2.29-2.410.22151340.18496240X-RAY DIFFRACTION98.98
2.41-2.560.21571340.18636304X-RAY DIFFRACTION99.49
2.56-2.760.23771350.18736355X-RAY DIFFRACTION99.57
2.76-3.040.24371350.19196292X-RAY DIFFRACTION98.77
3.04-3.480.21811360.17796369X-RAY DIFFRACTION99.34
3.48-4.380.16761360.15516385X-RAY DIFFRACTION98.65
4.38-38.050.21091420.17356644X-RAY DIFFRACTION98.92

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