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- PDB-8eei: Unbound C. ammoniagenes monoamine oxidase (MAO) -

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Basic information

Entry
Database: PDB / ID: 8eei
TitleUnbound C. ammoniagenes monoamine oxidase (MAO)
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / Monoamine / oxidase
Function / homologyAmine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / 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 1.2Oct 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
A: Amine oxidase
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6164
Polymers100,0452
Non-polymers1,5712
Water15,331851
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-32 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.995, 118.855, 141.094
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 51.08 %
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: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.78→38.14 Å / Num. obs: 96976 / % possible obs: 99.54 % / Redundancy: 10.3 % / Biso Wilson estimate: 15.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.052 / Rrim(I) all: 0.167 / Net I/σ(I): 14.2
Reflection shellResolution: 1.78→1.844 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.547 / Mean I/σ(I) obs: 2 / Num. unique obs: 9316 / CC1/2: 0.695 / Rpim(I) all: 0.518 / Rrim(I) all: 1.634 / % possible all: 96.93

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CR0

6cr0


Resolution: 1.78→38.14 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2066 1353 1.4 %
Rwork0.1855 95425 -
obs0.1858 96778 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.86 Å2
Refinement stepCycle: LAST / Resolution: 1.78→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6872 0 106 851 7829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00867153
X-RAY DIFFRACTIONf_angle_d1.02449752
X-RAY DIFFRACTIONf_chiral_restr0.09031044
X-RAY DIFFRACTIONf_plane_restr0.00581252
X-RAY DIFFRACTIONf_dihedral_angle_d19.29262482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.840.27131300.23399176X-RAY DIFFRACTION97.03
1.84-1.920.23891340.21519475X-RAY DIFFRACTION99.93
1.92-2.010.21681340.20249472X-RAY DIFFRACTION99.95
2.01-2.110.26011350.19159454X-RAY DIFFRACTION99.46
2.11-2.240.2041350.19089494X-RAY DIFFRACTION99.88
2.24-2.420.21331350.19119519X-RAY DIFFRACTION99.89
2.42-2.660.20661350.19459547X-RAY DIFFRACTION99.79
2.66-3.050.23831360.19159604X-RAY DIFFRACTION99.98
3.05-3.840.18681370.17289680X-RAY DIFFRACTION99.86
3.84-38.140.16551420.162610004X-RAY DIFFRACTION99.85

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