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- PDB-5lti: Crystal structure of the alpha subunit of heme dependent oxidativ... -

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Basic information

Entry
Database: PDB / ID: 5lti
TitleCrystal structure of the alpha subunit of heme dependent oxidative N-demethylase (HODM) in complex with the dimethylamine substrate
Componentsheme dependent oxidative N-demethylase
KeywordsOXIDOREDUCTASE / heme binding / PAS domain / amine oxidase / dimethylamine
Function / homology
Function and homology information


dimethylamine monooxygenase / oxidoreductase activity / metal ion binding
Similarity search - Function
Haem-dependent oxidative N-demethylase, alpha subunit-like / Haem-dependent oxidative N-demethylase, alpha subunit-like
Similarity search - Domain/homology
DIMETHYLAMINE / PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / DI(HYDROXYETHYL)ETHER / Heme-dependent oxidative N-demethylase alpha subunit
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsOrtmayer, M. / Leys, D.
CitationJournal: Nature / Year: 2016
Title: An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme.
Authors: Ortmayer, M. / Lafite, P. / Menon, B.R. / Tralau, T. / Fisher, K. / Denkhaus, L. / Scrutton, N.S. / Rigby, S.E. / Munro, A.W. / Hay, S. / Leys, D.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Dec 21, 2016Group: Database references
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heme dependent oxidative N-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9826
Polymers40,1621
Non-polymers8215
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-25 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.212, 80.212, 144.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-505-

NA

21A-784-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein heme dependent oxidative N-demethylase


Mass: 40161.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: Pmen_3455 / Production host: Escherichia coli (E. coli) / References: UniProt: A4XXY9

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Non-polymers , 6 types, 198 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DMN / DIMETHYLAMINE


Mass: 45.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7N
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: The HODM-heme subunit was crystallised at 3 mg ml-1 in 50 mM KPi, 100 mM KCl, pH 7.5. Initial crystallisation conditions were identified using the JCSG+ matrix screen (Molecular dimensions). ...Details: The HODM-heme subunit was crystallised at 3 mg ml-1 in 50 mM KPi, 100 mM KCl, pH 7.5. Initial crystallisation conditions were identified using the JCSG+ matrix screen (Molecular dimensions). Crystals suitable for diffraction experiments were obtained by sitting drop vapour diffusion at 277 K in 400 nL drops containing equal volumes of protein and a solution containing 30% PEG 2K MME and 0.1 M potassium thiocyanate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.9→28.36 Å / Num. obs: 36266 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 12 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LTE

5lte


Resolution: 1.9→28.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.325 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20101 1909 5 %RANDOM
Rwork0.17283 ---
obs0.17424 36235 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.824 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.9→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 54 193 2985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192898
X-RAY DIFFRACTIONr_bond_other_d0.0010.022675
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.9683952
X-RAY DIFFRACTIONr_angle_other_deg0.96136113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64322.484153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30815455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9821533
X-RAY DIFFRACTIONr_chiral_restr0.140.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213312
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02747
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 137 -
Rwork0.211 2623 -
obs--100 %

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