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- PDB-4usr: Structure of flavin-containing monooxygenase from Pseudomonas stu... -

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Basic information

Entry
Database: PDB / ID: 4usr
TitleStructure of flavin-containing monooxygenase from Pseudomonas stutzeri NF13
ComponentsMONOOXYGENASE
KeywordsOXIDOREDUCTASE / FAD / MONOOXYGENASE / NAD(P)H
Function / homology
Function and homology information


monooxygenase activity / flavin adenine dinucleotide binding
Similarity search - Function
: / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Monooxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS STUTZERI NF13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsJensen, C.N. / Ali, S.T. / Allen, M.J. / Grogan, G.
CitationJournal: J.Mol.Catal. / Year: 2014
Title: Exploring Nicotinamide Cofactor Promiscuity in Nad(P)H-Dependent Flavin Containing Monooxygenases (Fmos) Using Natural Variation within the Phosphate Binding Loop. Structure and Activity of ...Title: Exploring Nicotinamide Cofactor Promiscuity in Nad(P)H-Dependent Flavin Containing Monooxygenases (Fmos) Using Natural Variation within the Phosphate Binding Loop. Structure and Activity of Fmos from Cellvibrio Sp. Br and Pseudomonas Stutzeri NF13
Authors: Jensen, C.N. / Ali, S.T. / Allen, M.J. / Grogan, G.
History
DepositionJul 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7573
Polymers39,8791
Non-polymers8782
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.560, 63.560, 189.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MONOOXYGENASE / FLAVIN-CONTAINING MONOOXYGENASE


Mass: 39878.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS STUTZERI NF13 (bacteria) / Description: SYNTHETIC GENE / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: M2V3J0, EC: 1.14.13.8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.84 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7 / Details: 35 % (W/V) TACSIMATE AT PH 7.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862
DetectorDate: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.83→35.94 Å / Num. obs: 41893 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9
Reflection shellResolution: 1.83→1.85 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A9W

4a9w


Resolution: 1.83→35.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.306 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20433 2028 5 %RANDOM
Rwork0.16232 ---
obs0.16438 38217 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.953 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.83→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 59 211 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192933
X-RAY DIFFRACTIONr_bond_other_d0.0020.022705
X-RAY DIFFRACTIONr_angle_refined_deg2.1551.974039
X-RAY DIFFRACTIONr_angle_other_deg1.09536204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.522.52127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15915417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3571529
X-RAY DIFFRACTIONr_chiral_restr0.1860.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02693
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_it2.0461.8781447
X-RAY DIFFRACTIONr_mcbond_other2.0461.8771446
X-RAY DIFFRACTIONr_mcangle_it2.9152.8051812
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7952.0751486
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: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 144 -
Rwork0.198 2772 -
obs--99.93 %

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