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- PDB-8een: C. ammoniagenes monoamine oxidase (MAO) C424S variant -

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Basic information

Entry
Database: PDB / ID: 8een
TitleC. ammoniagenes monoamine oxidase (MAO) C424S variant
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / Monoamine / oxidase / flavoenzyme
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: 1.46 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
B: Amine oxidase
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5604
Polymers99,9892
Non-polymers1,5712
Water15,583865
1
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7802
Polymers49,9941
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7802
Polymers49,9941
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.229, 117.835, 141.479
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: 49994.355 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-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.: 865 / 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: 51.01 %
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: Aug 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.46→29.83 Å / Num. obs: 173307 / % possible obs: 99.51 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.041 / Rrim(I) all: 0.105 / Net I/σ(I): 11.8
Reflection shellResolution: 1.46→1.514 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 16432 / CC1/2: 0.732 / Rpim(I) all: 0.998 / Rrim(I) all: 0.651 / % possible all: 95.37

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→29.83 Å / SU ML: 0.1448 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2047 2000 1.15 %
Rwork0.1854 171303 -
obs0.1856 173303 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.6 Å2
Refinement stepCycle: LAST / Resolution: 1.46→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6882 0 106 865 7853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00757178
X-RAY DIFFRACTIONf_angle_d0.96699791
X-RAY DIFFRACTIONf_chiral_restr0.08621047
X-RAY DIFFRACTIONf_plane_restr0.00531260
X-RAY DIFFRACTIONf_dihedral_angle_d12.9739954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.251330.252611411X-RAY DIFFRACTION93.57
1.5-1.540.26151430.229712194X-RAY DIFFRACTION99.97
1.54-1.580.24591410.21212139X-RAY DIFFRACTION99.98
1.58-1.640.23421420.205212187X-RAY DIFFRACTION100
1.64-1.690.23521430.198512158X-RAY DIFFRACTION99.98
1.69-1.760.22821430.196312227X-RAY DIFFRACTION100
1.76-1.840.20791420.192812217X-RAY DIFFRACTION100
1.84-1.940.20131430.185312259X-RAY DIFFRACTION99.99
1.94-2.060.18921420.182112221X-RAY DIFFRACTION100
2.06-2.220.17831440.182312299X-RAY DIFFRACTION100
2.22-2.440.1911440.184312310X-RAY DIFFRACTION99.98
2.44-2.80.20381450.18812356X-RAY DIFFRACTION100
2.8-3.520.21871460.183312486X-RAY DIFFRACTION99.99
3.52-29.830.18361490.161112839X-RAY DIFFRACTION99.94

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