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- PDB-8p84: X-ray structure of Thermoanaerobacterales bacterium monoamine oxidase -

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Basic information

Entry
Database: PDB / ID: 8p84
TitleX-ray structure of Thermoanaerobacterales bacterium monoamine oxidase
ComponentsMonoamine oxidase
KeywordsFLAVOPROTEIN / monoamine oxidase / Thermoanaerobacterales bacterium / enzyme / n-hexylamine
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesThermoanaerobacterales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBasile, L. / Santema, L.L. / Fraaije, M.W. / Binda, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationECS00000036 Italy
CitationJournal: Febs J. / Year: 2024
Title: Discovery and structural characterization of a thermostable bacterial monoamine oxidase.
Authors: Santema, L.L. / Basile, L. / Binda, C. / Fraaije, M.W.
History
DepositionMay 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,9168
Polymers100,1802
Non-polymers1,7366
Water12,178676
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-48 kcal/mol
Surface area30070 Å2
Unit cell
Length a, b, c (Å)67.931, 94.167, 127.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Monoamine oxidase


Mass: 50089.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterales bacterium (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG4000, 100 mM tris buffer pH 8.5, 200 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.5→47.13 Å / Num. obs: 131032 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Net I/σ(I): 17.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.158 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6419 / CC1/2: 0.689 / Rpim(I) all: 0.709 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.13 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.297 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18549 6435 4.9 %RANDOM
Rwork0.159 ---
obs0.16028 124503 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-0 Å2
2--0.2 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.5→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6715 0 115 676 7506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0137014
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176465
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.6679624
X-RAY DIFFRACTIONr_angle_other_deg2.0311.58514814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.37920.398377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9961570
X-RAY DIFFRACTIONr_chiral_restr0.0920.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021604
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5311.7633595
X-RAY DIFFRACTIONr_mcbond_other1.5231.7613593
X-RAY DIFFRACTIONr_mcangle_it2.1482.6444492
X-RAY DIFFRACTIONr_mcangle_other2.1482.6434492
X-RAY DIFFRACTIONr_scbond_it2.9562.0513419
X-RAY DIFFRACTIONr_scbond_other2.9562.053420
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3282.9645133
X-RAY DIFFRACTIONr_long_range_B_refined5.06622.0348034
X-RAY DIFFRACTIONr_long_range_B_other5.01521.6617884
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 6605 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.360.5
Bmedium thermal2.522
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 480 -
Rwork0.388 9108 -
obs--99.91 %

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