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- PDB-3x0x: Crystal structure of apo-DszC from Rhodococcus erythropolis D-1 -

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Basic information

Entry
Database: PDB / ID: 3x0x
TitleCrystal structure of apo-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
Dibenzothiophene monooxygenase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 / Category: citation / citation_author / database_2
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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)361,1608
Polymers361,1608
Non-polymers00
Water24,6811370
1
A: DszC
B: DszC
D: DszC
C: DszC


Theoretical massNumber of molelcules
Total (without water)180,5804
Polymers180,5804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-88 kcal/mol
Surface area55100 Å2
MethodPISA
2
E: DszC
F: DszC
G: DszC
H: DszC


Theoretical massNumber of molelcules
Total (without water)180,5804
Polymers180,5804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-88 kcal/mol
Surface area55330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.130, 123.250, 184.270
Angle α, β, γ (deg.)90.00, 101.21, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1370 / 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: 45.42 %
Crystal growTemperature: 293 K / pH: 6
Details: 0.2M Malonate (pH 6.0), 24% (w/v) PEG 3350, 50mM NaF, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. all: 182743 / Num. obs: 179463 / % possible obs: 98.2 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.11→2.24 Å / % possible all: 95.8

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→43.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.115 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25256 8996 5 %RANDOM
Rwork0.18608 ---
obs0.18938 170464 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.025 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.03 Å2
2--0.05 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.11→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24432 0 0 1370 25802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01925032
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.92934136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06553192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30723.7581192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.235153680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.97315184
X-RAY DIFFRACTIONr_chiral_restr0.1160.23712
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02119720
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: 2.114→2.169 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 626 -
Rwork0.231 11657 -
obs--92.77 %

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