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- PDB-6ll1: Oxygen-exposed reduced terminal oxygenase in carbazole 1,9a-dioxy... -

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Basic information

Entry
Database: PDB / ID: 6ll1
TitleOxygen-exposed reduced terminal oxygenase in carbazole 1,9a-dioxygenase
ComponentsTerminal oxygenase component of carbazole
KeywordsOXIDOREDUCTASE / oxygen-exposed
Function / homology
Function and homology information


: / organonitrogen compound catabolic process / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Homotrimeric ring hydroxylase, catalytic domain / Homotrimeric ring hydroxylase / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / OXYGEN MOLECULE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Terminal oxygenase component of carbazole
Similarity search - Component
Biological speciesJanthinobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: To Be Published
Title: Oxygen-exposed reduced terminal oxygenase in carbazole 1,9a-dioxygenase
Authors: Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
History
DepositionDec 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminal oxygenase component of carbazole
B: Terminal oxygenase component of carbazole
C: Terminal oxygenase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,65136
Polymers134,7323
Non-polymers2,91833
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15080 Å2
ΔGint-90 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.738, 91.738, 240.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Terminal oxygenase component of carbazole


Mass: 44910.738 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janthinobacterium sp. (strain J3) (bacteria)
Strain: J3 / Gene: carAa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84II6

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Non-polymers , 9 types, 481 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M MgCl2, 0.1 M HEPES pH 7.5, 30% (v/v) PEG MME 550

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→80 Å / Num. obs: 61883 / % possible obs: 100 % / Redundancy: 22.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 39.5
Reflection shellResolution: 2.15→2.19 Å / Rmerge(I) obs: 0.722 / Num. unique obs: 3101

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WW9

1ww9


Resolution: 2.15→79.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.828 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20898 3074 5.1 %RANDOM
Rwork0.15269 ---
obs0.1556 57710 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.509 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å2-0 Å2
2---0.11 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.15→79.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9243 0 158 448 9849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0199621
X-RAY DIFFRACTIONr_bond_other_d0.0020.028800
X-RAY DIFFRACTIONr_angle_refined_deg1.861.95112985
X-RAY DIFFRACTIONr_angle_other_deg1.064320482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80851148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47724.81474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.129151603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5411548
X-RAY DIFFRACTIONr_chiral_restr0.1110.21349
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110576
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021936
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_it2.4132.7054595
X-RAY DIFFRACTIONr_mcbond_other2.4122.7044594
X-RAY DIFFRACTIONr_mcangle_it3.7024.0435739
X-RAY DIFFRACTIONr_mcangle_other3.7024.0445740
X-RAY DIFFRACTIONr_scbond_it2.8952.9685026
X-RAY DIFFRACTIONr_scbond_other2.8952.9695027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5194.37240
X-RAY DIFFRACTIONr_long_range_B_refined6.25231.17710890
X-RAY DIFFRACTIONr_long_range_B_other6.25231.18310891
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 186 -
Rwork0.171 3705 -
obs--85.52 %

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