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- PDB-6llh: Biphenyl-2,3-diol-soaked resting complex of Oxy and Fd in carbazo... -

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Basic information

Entry
Database: PDB / ID: 6llh
TitleBiphenyl-2,3-diol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase
Components
  • Ferredoxin CarAc
  • Terminal oxygenase component of carbazole
KeywordsOXIDOREDUCTASE / complex / dioxygenase / ligand-bound
Function / homology
Function and homology information


carbazole catabolic process / ferredoxin hydrogenase activity / dioxygenase activity / 2 iron, 2 sulfur cluster binding / 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
ACETATE ION / BIPHENYL-2,3-DIOL / : / FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Terminal oxygenase component of carbazole / Ferredoxin CarAc
Similarity search - Component
Biological speciesJanthinobacterium sp.
Pseudomonas resinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: To Be Published
Title: Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase
Authors: Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
History
DepositionDec 23, 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
D: Ferredoxin CarAc
E: Ferredoxin CarAc
F: Ferredoxin CarAc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,24835
Polymers172,0766
Non-polymers3,17229
Water18,7361040
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17760 Å2
ΔGint-205 kcal/mol
Surface area56730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.257, 89.793, 105.445
Angle α, β, γ (deg.)90.000, 103.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ABCDEF

#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
#2: Protein Ferredoxin CarAc / Carbazole 1 / 9a-dioxygenase / ferredoxin component / CARDO


Mass: 12448.059 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas resinovorans (bacteria) / Gene: carAc / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GI16

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Non-polymers , 9 types, 1069 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-BPY / BIPHENYL-2,3-DIOL


Mass: 186.207 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H10O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.05 M Bis-Tris pH 5.5, 0.1 M Ammonium Acetate, 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 121104 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 24
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 121194 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DE5

2de5


Resolution: 1.99→36.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.549 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.143
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.207 6097 5.1 %RANDOM
Rwork0.162 ---
obs0.1643 113684 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.7 Å2 / Biso mean: 30.155 Å2 / Biso min: 11.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0.18 Å2
2--0.03 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.99→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11722 0 160 1040 12922
Biso mean--48.86 35.94 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01412265
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710925
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.66316613
X-RAY DIFFRACTIONr_angle_other_deg0.9311.65625621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07751500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50323.194648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.555152018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5551563
X-RAY DIFFRACTIONr_chiral_restr0.0780.21513
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022301
LS refinement shellResolution: 1.993→2.045 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 404 -
Rwork0.22 7771 -
all-8175 -
obs--91.28 %

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