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

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Basic information

Entry
Database: PDB / ID: 5lte
TitleCrystal structure of the alpha subunit of heme dependent oxidative N-demethylase (HODM)
Componentsheme dependent oxidative N-demethylase
KeywordsOXIDOREDUCTASE / heme binding / PAS domain / amine oxidase
Function / homologyHaem-dependent oxidative N-demethylase, alpha subunit-like / Haem-dependent oxidative N-demethylase, alpha subunit-like / metal ion binding / 2-ETHOXYETHANOL / PROTOPORPHYRIN IX CONTAINING FE / DUF3445 domain-containing protein
Function and homology information
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.65 Å
AuthorsOrtmayer, M. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBBE0170101 United Kingdom
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 1.4Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,8914
Polymers40,1621
Non-polymers7303
Water5,783321
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-26 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.908, 79.908, 144.712
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-503-

NA

21A-692-

HOH

31A-906-

HOH

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Components

#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 (strain ymp) (bacteria)
Strain: ymp / Gene: Pmen_3455 / Production host: Escherichia coli (E. coli) / References: UniProt: A4XXY9
#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-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
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 PILATUS3 X 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: 1.65→26.82 Å / Num. obs: 53715 / % possible obs: 99.93 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.4
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.65→26.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.333 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19359 2872 5.1 %RANDOM
Rwork0.16341 ---
obs0.16493 53715 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.861 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.65→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 49 321 3103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192902
X-RAY DIFFRACTIONr_bond_other_d0.0020.022672
X-RAY DIFFRACTIONr_angle_refined_deg2.231.9673962
X-RAY DIFFRACTIONr_angle_other_deg1.01736109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5495338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96822.532154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77815456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2581533
X-RAY DIFFRACTIONr_chiral_restr0.1580.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213332
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02751
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: 1.655→1.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 224 -
Rwork0.198 3876 -
obs--100 %

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