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- PDB-6llk: Biphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a... -

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Basic information

Entry
Database: PDB / ID: 6llk
TitleBiphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase
ComponentsTerminal oxygenase component of carbazole
KeywordsOXIDOREDUCTASE / dioxygenase / ligand-bound
Function / homology
Function and homology information


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
: / FE2/S2 (INORGANIC) CLUSTER / 3-(2-hydroxyphenyl)benzene-1,2-diol / Terminal oxygenase component of carbazole
Similarity search - Component
Biological speciesJanthinobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 terminal oxygenase of 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

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Assembly

Deposited unit
A: Terminal oxygenase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5416
Polymers44,9111
Non-polymers6305
Water5,026279
1
A: Terminal oxygenase component of carbazole
hetero molecules

A: Terminal oxygenase component of carbazole
hetero molecules

A: Terminal oxygenase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,62318
Polymers134,7323
Non-polymers1,89115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area11850 Å2
ΔGint-108 kcal/mol
Surface area42630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.361, 131.361, 131.361
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Terminal oxygenase component of carbazole


Mass: 44910.738 Da / Num. of mol.: 1
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 , 6 types, 284 molecules

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


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-WBP / 3-(2-hydroxyphenyl)benzene-1,2-diol


Mass: 202.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 4.21 Å3/Da / Density % sol: 70.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.2, 15-17.5% MPD

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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 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 33834 / % possible obs: 100 % / Redundancy: 22.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 39.8
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.353 / Num. unique obs: 33834

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WW9

1ww9


Resolution: 2.3→29.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.241 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.157
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 1672 5 %RANDOM
Rwork0.1603 ---
obs0.1624 31820 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.07 Å2 / Biso mean: 35.695 Å2 / Biso min: 16.17 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.3→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 32 279 3419
Biso mean--57.35 39.54 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143241
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172881
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.6644397
X-RAY DIFFRACTIONr_angle_other_deg0.9551.6516756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10223.167180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57715546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1411518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023631
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02613
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.243 114 -
Rwork0.227 2279 -
obs--98.6 %

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