[English] 日本語
Yorodumi
- PDB-4jek: Structure of dibenzothiophene monooxygenase (DszC) from Rhodococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jek
TitleStructure of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis
ComponentsDibenzothiophene desulfurization enzyme C
KeywordsOXIDOREDUCTASE / Dibenzothiophene desulfurization enzyme C
Function / homology
Function and homology information


dibenzothiophene catabolic process / oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
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, 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 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 desulfurization enzyme C
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsZhang, L. / Duan, X.L. / Zhou, D.M. / Li, X.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization and preliminary structural analysis of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis
Authors: Duan, X. / Zhang, L. / Zhou, D. / Ji, K. / Ma, T. / Shui, W. / Li, G. / Li, X.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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


Theoretical massNumber of molelcules
Total (without water)391,2338
Polymers391,2338
Non-polymers00
Water10,269570
1
A: Dibenzothiophene desulfurization enzyme C
F: Dibenzothiophene desulfurization enzyme C
G: Dibenzothiophene desulfurization enzyme C
H: Dibenzothiophene desulfurization enzyme C


Theoretical massNumber of molelcules
Total (without water)195,6164
Polymers195,6164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14060 Å2
ΔGint-91 kcal/mol
Surface area53830 Å2
MethodPISA
2
B: Dibenzothiophene desulfurization enzyme C
C: Dibenzothiophene desulfurization enzyme C
D: Dibenzothiophene desulfurization enzyme C
E: Dibenzothiophene desulfurization enzyme C


Theoretical massNumber of molelcules
Total (without water)195,6164
Polymers195,6164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14020 Å2
ΔGint-91 kcal/mol
Surface area53820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.160, 96.270, 98.563
Angle α, β, γ (deg.)81.03, 67.57, 85.84
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 19:417 )
211chain B and (resseq 19:417 )
311chain C and (resseq 19:417 )
411chain D and (resseq 19:417 )
511chain E and (resseq 19:417 )
611chain F and (resseq 19:417 )
711chain G and (resseq 19:417 )
811chain H and (resseq 19:417 )

-
Components

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


Mass: 48904.117 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: IGTS8 / Gene: soxC, dszC / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P54998
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17.5% PEG3350, 200mM Bis-Tris, 200mM (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U11.005
SYNCHROTRONPhoton Factory BL-5A20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMar 1, 2012
RAYONIX MX-2252CCDJan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0051
20.9791
ReflectionResolution: 2.4→40 Å / Num. all: 127397 / Num. obs: 122302 / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.5 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.4-2.49195.9
2.49-2.59196.1
2.59-2.7196.5
2.7-2.85197
2.85-3.02196.8
3.02-3.26196.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→40 Å / SU ML: 0.78 / σ(F): 1.96 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 6118 5.01 %RANDOM
Rwork0.2069 ---
obs0.2089 122103 96.21 %-
all-122631 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.345 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.8161 Å27.61 Å23.1791 Å2
2---9.0435 Å25.9699 Å2
3---16.8596 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24328 0 0 570 24898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01424928
X-RAY DIFFRACTIONf_angle_d1.24934000
X-RAY DIFFRACTIONf_dihedral_angle_d15.8888744
X-RAY DIFFRACTIONf_chiral_restr0.0833704
X-RAY DIFFRACTIONf_plane_restr0.0064520
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3041X-RAY DIFFRACTIONPOSITIONAL
12B3041X-RAY DIFFRACTIONPOSITIONAL0.121
13C3041X-RAY DIFFRACTIONPOSITIONAL0.112
14D3041X-RAY DIFFRACTIONPOSITIONAL0.102
15E3041X-RAY DIFFRACTIONPOSITIONAL0.082
16F3041X-RAY DIFFRACTIONPOSITIONAL0.111
17G3041X-RAY DIFFRACTIONPOSITIONAL0.103
18H3041X-RAY DIFFRACTIONPOSITIONAL0.088
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.42260.30461530.2825266867
2.4226-2.45110.36711970.2898389597
2.4511-2.4810.35832190.2868389897
2.481-2.51240.30652130.2746389497
2.5124-2.54540.32432130.2717386897
2.5454-2.58030.32842130.256389297
2.5803-2.61720.30592050.2433388697
2.6172-2.65620.31712190.2408391397
2.6562-2.69770.30092210.247386097
2.6977-2.74190.30881970.2339394497
2.7419-2.78920.27211790.239389297
2.7892-2.83990.30712250.2322394598
2.8399-2.89450.30932170.2283389098
2.8945-2.95360.31692070.2334387597
2.9536-3.01780.28782090.2263396297
3.0178-3.0880.29211930.2264391298
3.088-3.16510.25412180.2177389297
3.1651-3.25070.29451900.2225389897
3.2507-3.34630.2691780.2225396398
3.3463-3.45430.25892050.2112389597
3.4543-3.57760.22542000.2081390397
3.5776-3.72080.22762150.2037389397
3.7208-3.890.23611870.1914390597
3.89-4.09490.21491940.176389396
4.0949-4.35120.19752150.1716389197
4.3512-4.68670.19851810.1821378394
4.6867-5.15750.20872060.1832390397
5.1575-5.90180.19782210.20593979100
5.9018-7.42820.21241960.18984043100
7.4282-400.18832320.1597395099

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more