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- PDB-3x0y: Crystal structure of FMN-bound DszC from Rhodococcus erythropolis D-1 -

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Basic information

Entry
Database: PDB / ID: 3x0y
TitleCrystal structure of FMN-bound DszC from Rhodococcus erythropolis D-1
ComponentsDszC
KeywordsOXIDOREDUCTASE / DBT monooxygenase / desulfurization / acyl-CoA dehydrogenase domain / FMN-dependent
Function / homology
Function and homology information


dibenzothiophene catabolic process / dibenzothiophene monooxygenase / oxidoreductase activity, acting on the CH-CH group of donors / monooxygenase activity / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain ...Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Dibenzothiophene monooxygenase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuan, L.J. / Lee, W.C. / Wang, S.P. / Ohtsuka, J. / Tanokura, M.
CitationJournal: Febs J. / Year: 2015
Title: Crystal structures of apo-DszC and FMN-bound DszC from Rhodococcus erythropolis D-1.
Authors: Guan, L.J. / Lee, W.C. / Wang, S. / Ohshiro, T. / Izumi, Y. / Ohtsuka, J. / Tanokura, M.
History
DepositionOct 23, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DszC
B: DszC
C: DszC
D: DszC
E: DszC
F: DszC
G: DszC
H: DszC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,98612
Polymers361,1608
Non-polymers1,8254
Water14,322795
1
A: DszC
F: DszC
G: DszC
H: DszC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4936
Polymers180,5804
Non-polymers9132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16660 Å2
ΔGint-112 kcal/mol
Surface area54740 Å2
MethodPISA
2
B: DszC
C: DszC
D: DszC
E: DszC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4936
Polymers180,5804
Non-polymers9132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16830 Å2
ΔGint-108 kcal/mol
Surface area54080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.480, 123.520, 184.520
Angle α, β, γ (deg.)90.00, 101.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DszC / monooxygenase


Mass: 45145.023 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: D-1 / Gene: dszC / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A0C6DRW4*PLUS
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE HAS BEEN DEPOSITED TO GENBANK WITH ACCESSION NUMBER LC027463.1

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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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Malonate (pH 6.0), 24% (w/v) PEG 3350, 50mM NaF, 1mM FMN, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 141218 / Num. obs: 140320 / % possible obs: 99.4 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.44 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.38 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.873 / SU B: 19.337 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27232 7038 5 %RANDOM
Rwork0.22953 ---
obs0.23165 133279 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.111 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å21.55 Å2
2---1.46 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24462 0 124 795 25381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01925215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0223194
X-RAY DIFFRACTIONr_angle_refined_deg0.8671.93534410
X-RAY DIFFRACTIONr_angle_other_deg0.708353105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.34653202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80423.7571195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.754153683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.93315185
X-RAY DIFFRACTIONr_chiral_restr0.0470.23731
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02129514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026091
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_it0.3931.84812826
X-RAY DIFFRACTIONr_mcbond_other0.3931.84812825
X-RAY DIFFRACTIONr_mcangle_it0.7332.77116022
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.2031.88912389
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: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 519 -
Rwork0.277 9127 -
obs--92.56 %
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)
10.5072-0.2389-0.36060.50980.07760.3209-0.03440.0487-0.01010.00540.0034-0.10680.083-0.08470.03110.15360.0171-0.10230.3138-0.00850.1935-98.22426.62732.659
20.3118-0.19710.09440.62510.09070.11260.16940.1053-0.0129-0.1152-0.21780.07280.03930.02750.04840.1780.1004-0.12820.3804-0.02160.1797-129.70566.12515.157
30.785-0.2327-0.29150.14490.10290.24740.04540.08520.15720.0144-0.0452-0.14270.0192-0.0558-0.00030.07560.0642-0.05890.31690.08230.303-89.43570.09824.964
40.4779-0.58310.1531.1769-0.15250.060.01450.03640.22160.0173-0.0648-0.2260.0143-0.02840.05030.0850.0617-0.0870.29550.04620.3423-127.34105.09329.065
50.3775-0.2518-0.15360.4127-0.18470.5851-0.1429-0.06670.15370.20460.0694-0.1224-0.06490.00060.07350.20020.0589-0.16570.3137-0.05560.2219-108.33883.71859.247
60.5618-0.1499-0.1490.11250.09670.48720.08480.0594-0.03330.0806-0.09380.01730.048-0.20040.0090.1793-0.0869-0.05180.3875-0.0270.1655-133.88633.88552.197
70.30770.29130.26720.38320.40480.55070.08920.0004-0.04590.17430.0283-0.16430.0786-0.0027-0.11750.26880.0209-0.23610.3268-0.00330.2299-85.33641.26569.332
80.37890.3177-0.19740.9514-0.34190.40840.0537-0.0798-0.05850.3941-0.1175-0.01780.0716-0.05290.06380.588-0.1404-0.08180.32890.03670.0686-111.98711.67280.056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 500
2X-RAY DIFFRACTION2B18 - 417
3X-RAY DIFFRACTION3C18 - 500
4X-RAY DIFFRACTION4D16 - 500
5X-RAY DIFFRACTION5E17 - 417
6X-RAY DIFFRACTION6F18 - 500
7X-RAY DIFFRACTION7G17 - 417
8X-RAY DIFFRACTION8H18 - 417

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