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- PDB-7rt0: 1.80 A resolution structure of MAO from P. nicotinovorans in comp... -

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Basic information

Entry
Database: PDB / ID: 7rt0
Title1.80 A resolution structure of MAO from P. nicotinovorans in complex with FAD
Components4-methylaminobutanoate oxidase (methylamine-forming)
KeywordsOXIDOREDUCTASE / MAO / FAD binding / amine oxidase / flavin oxidase / N-methyl-GABA / GABA
Function / homology4-methylaminobutanoate oxidase (methylamine-forming) / nicotine catabolic process / : / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / 4-methylaminobutanoate oxidase (methylamine-forming)
Function and homology information
Biological speciesPaenarthrobacter nicotinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.8 Å
AuthorsLovell, S. / Bowman, A. / Battaile, K.P. / Deay, D.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: To be determined
Authors: Bowman, A. / Deay, D.O. / Battaile, K.P. / Lovell, S.
History
DepositionAug 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1May 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: 4-methylaminobutanoate oxidase (methylamine-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4563
Polymers44,4761
Non-polymers9802
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)203.302, 51.740, 45.739
Angle α, β, γ (deg.)90.000, 92.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-761-

HOH

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Components

#1: Protein 4-methylaminobutanoate oxidase (methylamine-forming) / Gamma-N-methylaminobutyrate oxidase 2


Mass: 44475.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nicotinovorans (bacteria)
Gene: mao, ORF56 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRARE
References: UniProt: Q8GAJ0, 4-methylaminobutanoate oxidase (methylamine-forming)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.7 Å3/Da / Density % sol: 54.47 % / Mosaicity: 0.11 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 20% (w/v) PEG 6000, 0.1 M Bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.69 Å / Num. obs: 44295 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.56 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.145 / Net I/σ(I): 8.6 / Num. measured all: 303398 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.8-1.847.11.0111866426370.7572100
9-45.696.50.0724843850.99521.399

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å45.68 Å
Translation1.9 Å45.68 Å

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Processing

Software
NameVersionClassification
PHENIXdev_4273refinement
XDSdata reduction
Aimless0.7.7data scaling
CRANK2phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→45.69 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 2182 4.93 %
Rwork0.1689 42094 -
obs0.1701 44276 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.48 Å2 / Biso mean: 23.1997 Å2 / Biso min: 8.95 Å2
Refinement stepCycle: final / Resolution: 1.8→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 66 286 3131
Biso mean--18.23 29.81 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.840.24981340.23926482782
1.84-1.880.25661280.212525782706
1.88-1.930.22461280.226172745
1.93-1.980.22331220.177126542776
1.98-2.040.20541270.168525912718
2.04-2.110.2091240.176826242748
2.11-2.180.20331650.174626102775
2.18-2.270.19711290.166626192748
2.27-2.370.17671240.155426202744
2.37-2.50.22131270.150526502777
2.5-2.650.19581510.158426012752
2.65-2.860.16831800.172326112791
2.86-3.140.19551120.175226382750
3.14-3.60.18481490.167426442793
3.6-4.530.18681350.142826722807
4.54-45.690.17391470.178727172864

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