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- PDB-4ap3: Oxidized steroid monooxygenase bound to NADP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4ap3
TitleOxidized steroid monooxygenase bound to NADP
ComponentsSTEROID MONOOXYGENASE
KeywordsOXIDOREDUCTASE / BAEYER-VILLIGER
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Steroid monooxygenase
Similarity search - Component
Biological speciesRHODOCOCCUS RHODOCHROUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsFranceschini, S. / van Beek, H.L. / Martinoli, C. / Pennetta, A. / Fraaije, M.W. / Mattevi, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Exploring the Structural Basis of Substrate Preferences in Baeyer-Villiger Monooxygenases: Insight from Steroid Monooxygenase.
Authors: Franceschini, S. / Van Beek, H.L. / Pennetta, A. / Martinoli, C. / Fraaije, M.W. / Mattevi, A.
History
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Dec 20, 2023Group: 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: STEROID MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9345
Polymers60,2131
Non-polymers1,7214
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.750, 81.750, 228.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein STEROID MONOOXYGENASE


Mass: 60212.883 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS RHODOCHROUS (bacteria) / Plasmid: PET-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50641, EC: 1.14.13.54
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 345 TO LEU

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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: 3.25 Å3/Da / Density % sol: 62.22 % / Description: NONE
Crystal growpH: 6.2 / Details: 1.9M MGSO4, 0.1M MES PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9336
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9336 Å / Relative weight: 1
ReflectionResolution: 2.39→66.44 Å / Num. obs: 31403 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AOS

4aos


Resolution: 2.39→66.44 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.736 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-19, 232-235 AND 512-516 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.23874 1577 5 %RANDOM
Rwork0.20705 ---
obs0.20866 29739 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.973 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.39→66.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 81 146 4197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194169
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.9615696
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21622.932191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69815589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6541535
X-RAY DIFFRACTIONr_chiral_restr0.0910.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213252
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.392→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 111 -
Rwork0.291 1927 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4852-0.4189-0.70121.3157-0.13022.5148-0.1176-0.0279-0.24780.07160.11980.09680.1885-0.146-0.00230.056-0.0533-0.02890.28690.10170.0681-7.14814.185-17.882
24.5239-0.4310.00022.4495-1.00062.46860.06260.3056-0.9864-0.3081-0.1680.25020.683-0.22010.10540.2931-0.0020.05320.30220.00550.313912.874-3.846-23.805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 159
2X-RAY DIFFRACTION1A393 - 549
3X-RAY DIFFRACTION2A160 - 392

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