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- PDB-4doy: Crystal structure of Dibenzothiophene desulfurization enzyme C -

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Basic information

Entry
Database: PDB / ID: 4doy
TitleCrystal structure of Dibenzothiophene desulfurization enzyme C
ComponentsDibenzothiophene desulfurization enzyme C
KeywordsOXIDOREDUCTASE / monooxygenase
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 / 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 / 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 oxidase/dehydrogenase, middle domain superfamily / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.789 Å
AuthorsLiu, S. / Zhang, C. / Zhu, D. / Gu, L.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of DszC from Rhodococcus sp. XP at 1.79 angstrom
Authors: Liu, S. / Zhang, C. / Su, T. / Wei, T. / Zhu, D. / Wang, K. / Huang, Y. / Dong, Y. / Yin, K. / Xu, S. / Xu, P. / Gu, L.
History
DepositionFeb 12, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Dibenzothiophene desulfurization enzyme C
B: Dibenzothiophene desulfurization enzyme C
C: Dibenzothiophene desulfurization enzyme C
D: Dibenzothiophene desulfurization enzyme C
E: Dibenzothiophene desulfurization enzyme C
F: Dibenzothiophene desulfurization enzyme C
G: Dibenzothiophene desulfurization enzyme C
H: Dibenzothiophene desulfurization enzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)379,16721
Polymers377,9708
Non-polymers1,19713
Water49,0012720
1
A: Dibenzothiophene desulfurization enzyme C
C: Dibenzothiophene desulfurization enzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6774
Polymers94,4932
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-21 kcal/mol
Surface area30800 Å2
MethodPISA
2
B: Dibenzothiophene desulfurization enzyme C
E: Dibenzothiophene desulfurization enzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8616
Polymers94,4932
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-15 kcal/mol
Surface area32130 Å2
MethodPISA
3
D: Dibenzothiophene desulfurization enzyme C
F: Dibenzothiophene desulfurization enzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7695
Polymers94,4932
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-23 kcal/mol
Surface area30570 Å2
MethodPISA
4
G: Dibenzothiophene desulfurization enzyme C
H: Dibenzothiophene desulfurization enzyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8616
Polymers94,4932
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-14 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.519, 98.824, 111.465
Angle α, β, γ (deg.)98.46, 106.99, 107.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dibenzothiophene desulfurization enzyme C / Monooxygenase / DBT sulfur dioxygenase


Mass: 47246.258 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus (bacteria) / Strain: XP / Gene: dszC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WNP1, unspecific monooxygenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2720 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS, 25%(w/v) Polyethylene glycol 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.97623
SYNCHROTRONSSRF BL17U20.97916
Detector
TypeIDDetectorDate
RAYONIX MX-2251CCDJul 10, 2009
RAYONIX MX-2252CCDJul 10, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.976231
20.979161
ReflectionResolution: 1.789→50 Å / Num. all: 324571 / Num. obs: 324571 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.86 Å / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.789→35.423 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.18 / σ(F): 0.04 / Phase error: 21.33 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 15296 5.01 %RANDOM
Rwork0.1683 289714 --
obs0.1696 305010 89.7 %-
all-305010 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.766 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 107.76 Å2 / Biso mean: 30.5102 Å2 / Biso min: 9.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.8058 Å2-6.0017 Å25.9746 Å2
2--2.2009 Å2-6.4489 Å2
3---0.6049 Å2
Refinement stepCycle: LAST / Resolution: 1.789→35.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24392 0 72 2720 27184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625486
X-RAY DIFFRACTIONf_angle_d0.9734807
X-RAY DIFFRACTIONf_chiral_restr0.0663764
X-RAY DIFFRACTIONf_plane_restr0.0054658
X-RAY DIFFRACTIONf_dihedral_angle_d12.9278993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7894-1.80970.32243170.27256080639756
1.8097-1.8310.28924430.2518424886778
1.831-1.85330.27924530.2458495894879
1.8533-1.87680.27694490.23278568901779
1.8768-1.90150.26824610.2228588904980
1.9015-1.92750.24625020.20339469997188
1.9275-1.9550.22944930.19658968946183
1.955-1.98420.22314840.18949096958085
1.9842-2.01520.21724820.18789311979387
2.0152-2.04830.21715100.18049455996588
2.0483-2.08360.21675090.174995871009689
2.0836-2.12150.20865020.168196581016089
2.1215-2.16220.21535070.171196701017790
2.1622-2.20640.25150.171696741018990
2.2064-2.25430.20035310.1689100201055193
2.2543-2.30680.19335140.169197941030891
2.3068-2.36450.21285210.168699051042692
2.3645-2.42840.19685320.1644100481058093
2.4284-2.49980.19335310.1671100351056693
2.4998-2.58050.20725350.1698101921072794
2.5805-2.67270.19375310.1646101711070295
2.6727-2.77960.19525420.1698102851082796
2.7796-2.90610.19565440.1701104401098497
2.9061-3.05920.19665510.1739104141096597
3.0592-3.25080.19975540.175105061106098
3.2508-3.50160.19455590.1717105941115398
3.5016-3.85360.16485580.1522106231118199
3.8536-4.41030.15445570.1369105871114499
4.4103-5.5530.16995640.149106921125699
5.553-35.43020.1645450.1623103651091096

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