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- PDB-3w8x: The complex structure of EncM with trifluorotriketide -

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Basic information

Entry
Database: PDB / ID: 3w8x
TitleThe complex structure of EncM with trifluorotriketide
ComponentsPutative FAD-dependent oxygenase EncM
KeywordsOXIDOREDUCTASE / monooxygenase / flavin binding
Function / homology
Function and homology information


FAD binding / oxidoreductase activity / identical protein binding
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 6,6,6-trifluoro-1-phenylhexane-1,3,5-trione / Putative FAD-dependent oxygenase EncM
Similarity search - Component
Biological speciesStreptomyces maritimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTeufel, R. / Miyanaga, A. / Stull, F. / Michaudel, Q. / Louie, G. / Noel, J.P. / Baran, P.S. / Palfey, B. / Moore, B.S.
CitationJournal: Nature / Year: 2013
Title: Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement.
Authors: Teufel, R. / Miyanaga, A. / Michaudel, Q. / Stull, F. / Louie, G. / Noel, J.P. / Baran, P.S. / Palfey, B. / Moore, B.S.
History
DepositionMar 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative FAD-dependent oxygenase EncM
B: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0077
Polymers100,8272
Non-polymers2,1805
Water11,728651
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-30 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.246, 85.175, 79.363
Angle α, β, γ (deg.)90.00, 99.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative FAD-dependent oxygenase EncM


Mass: 50413.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces maritimus (bacteria) / Gene: encM / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KHK2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of one atom of oxygen (internal monooxygenases or ...References: UniProt: Q9KHK2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of one atom of oxygen (internal monooxygenases or internal mixed-function oxidases)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-FTK / 6,6,6-trifluoro-1-phenylhexane-1,3,5-trione


Mass: 258.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9F3O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2mM DTT, 0.1M HEPES-Na, 0.2M calcium acetate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010
RadiationMonochromator: double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 83280 / Num. obs: 83197 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.82→1.85 Å / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W8W

3w8w


Resolution: 1.82→48.52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.763 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19207 4148 5 %RANDOM
Rwork0.15299 ---
all0.15495 79372 --
obs0.15495 79007 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.336 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20.01 Å2
2---0.58 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.82→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7014 0 148 651 7813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197353
X-RAY DIFFRACTIONr_bond_other_d0.0010.026798
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.97610041
X-RAY DIFFRACTIONr_angle_other_deg1.058315564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33422.579318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.566151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3591564
X-RAY DIFFRACTIONr_chiral_restr0.20.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021730
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.822→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 293 -
Rwork0.229 5505 -
obs--94.77 %
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)
10.1037-0.0195-0.07160.08060.0570.16730.0002-0.01950.01160.00770.01440.01380.00770.0331-0.01470.002-0.0003-0.00520.0227-0.00090.05217.640913.812336.5798
20.0906-0.03320.01550.07950.04480.2321-0.00120.00710.0085-0.02310.00350.01460.01770.0497-0.00230.01550.0055-0.00490.01860.00250.038712.7728-0.11487.1348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 462
2X-RAY DIFFRACTION2B2 - 462

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