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- PDB-7bug: Reduced oxygenase of carbazole 1,9a-dioxygenase -

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Basic information

Entry
Database: PDB / ID: 7bug
TitleReduced oxygenase of carbazole 1,9a-dioxygenase
ComponentsTerminal oxygenase component of carbazole
KeywordsOXIDOREDUCTASE / ring-hydroxylating / dioxygenase
Function / homology
Function and homology information


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] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
CARBONATE ION / : / FE2/S2 (INORGANIC) CLUSTER / 2-METHOXYETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Terminal oxygenase component of carbazole
Similarity search - Component
Biological speciesJanthinobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMatsuzawa, J. / Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Noda Institute for Scientific Research Japan
CitationJournal: To Be Published
Title: Reduced oxygenase of carbazole 1,9a-dioxygenase
Authors: Matsuzawa, J. / Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
History
DepositionApr 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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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)138,94339
Polymers134,7323
Non-polymers4,21036
Water15,493860
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15700 Å2
ΔGint-116 kcal/mol
Surface area45200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.940, 91.940, 243.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 , 12 types, 896 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#11: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#12: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
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: 100 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 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 152740 / % possible obs: 100 % / Redundancy: 21.7 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 18.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.576 / Num. unique obs: 7547

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WW9

1ww9


Resolution: 1.6→46.01 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.709 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.082
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 7679 5 %RANDOM
Rwork0.1537 ---
obs0.1554 144934 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.56 Å2 / Biso mean: 21.3 Å2 / Biso min: 8.23 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.6→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9243 0 246 860 10349
Biso mean--42.54 32.46 -
Num. residues----1149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139909
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179140
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.64813383
X-RAY DIFFRACTIONr_angle_other_deg1.4631.59721328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25251200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43723.496532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.673151667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8151549
X-RAY DIFFRACTIONr_chiral_restr0.0920.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210975
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022028
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 623 -
Rwork0.263 10691 -
all-11314 -
obs--100 %

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