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- PDB-6llm: Biphenyl-2,3-diol-soaked terminal oxygenase of carbazole 1,9a-dio... -

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Basic information

Entry
Database: PDB / ID: 6llm
TitleBiphenyl-2,3-diol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase
ComponentsTerminal oxygenase component of carbazole
KeywordsOXIDOREDUCTASE / dioxygenase / ligand-bound
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
BIPHENYL-2,3-DIOL / : / FE2/S2 (INORGANIC) CLUSTER / Terminal oxygenase component of carbazole
Similarity search - Component
Biological speciesJanthinobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: To Be Published
Title: Biphenyl-2,3-diol-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)45,6517
Polymers44,9111
Non-polymers7406
Water7,260403
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)136,95321
Polymers134,7323
Non-polymers2,22118
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 area14400 Å2
ΔGint-137 kcal/mol
Surface area43460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.925, 130.925, 130.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-976-

HOH

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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, 409 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-BPY / BIPHENYL-2,3-DIOL


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 4.16 Å3/Da / Density % sol: 70.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.2-6.3, 15-20% MPD / PH range: 6.2-6.3

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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: 57678 / % possible obs: 98.1 % / Redundancy: 38.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 45.9
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.26 / Num. unique obs: 57678

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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: 1WW9

1ww9


Resolution: 1.9→46.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.355 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 2751 5.2 %RANDOM
Rwork0.1711 ---
obs0.1726 50334 90.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.71 Å2 / Biso mean: 26.153 Å2 / Biso min: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 39 403 3570
Biso mean--48.55 36.79 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143316
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172960
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.6644510
X-RAY DIFFRACTIONr_angle_other_deg1.0241.6556947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2215405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92323.115183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5031518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
LS refinement shellResolution: 1.902→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 205 -
Rwork0.269 3557 -
all-3762 -
obs--87.37 %

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