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- PDB-1ww9: Crystal structure of the terminal oxygenase component of carbazol... -

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Entry
Database: PDB / ID: 1ww9
TitleCrystal structure of the terminal oxygenase component of carbazole 1,9a-dioxygenase, a non-heme iron oxygenase system catalyzing the novel angular dioxygenation for carbazole and dioxin
Componentsterminal oxygenase component of carbazole
KeywordsOXIDOREDUCTASE / Terminal oxygenase / Carbazole 1 / 9a-dioxygenase / Angular dioxygenase / Rieske non-heme iron oxygenase system
Function / homology
Function and homology information


: / organonitrogen compound catabolic process / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
N-terminal domain of TfIIb - #680 / Homotrimeric ring hydroxylase, catalytic domain / Homotrimeric ring hydroxylase / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. ...N-terminal domain of TfIIb - #680 / Homotrimeric ring hydroxylase, catalytic domain / Homotrimeric ring hydroxylase / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single Sheet / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Terminal oxygenase component of carbazole
Similarity search - Component
Biological speciesJanthinobacterium sp. J3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsNojiri, H. / Ashikawa, Y. / Noguchi, H. / Nam, J.-W. / Urata, M. / Fujimoto, Z. / Mizuno, H. / Yoshida, T. / Habe, H. / Omori, T.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase
Authors: Nojiri, H. / Ashikawa, Y. / Noguchi, H. / Nam, J.-W. / Urata, M. / Fujimoto, Z. / Uchimura, H. / Terada, T. / Nakamura, S. / Shimizu, K. / Yoshida, T. / Habe, H. / Omori, T.
History
DepositionJan 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)45,1423
Polymers44,9111
Non-polymers2322
Water5,765320
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)135,4279
Polymers134,7323
Non-polymers6956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area10540 Å2
ΔGint-132 kcal/mol
Surface area44250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.914, 131.914, 131.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein terminal oxygenase component of carbazole / Terminal oxygenase component of carbazole 1 / 9a-dioxygenase


Mass: 44910.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janthinobacterium sp. J3 (bacteria) / Plasmid: pEJ3AaC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q84II6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 15-17.5% MPD, 0.1M MES, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9794, 0.9796, 0.9820
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 28, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.9821
ReflectionResolution: 1.95→14.94 Å / Num. obs: 54782 / % possible obs: 98.3 % / Biso Wilson estimate: 19 Å2
Reflection shellResolution: 1.95→2.02 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→14.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2543193.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2726 5 %RANDOM
Rwork0.194 ---
obs0.194 54782 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.8 Å2 / ksol: 0.379344 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.95→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 5 320 3461
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 443 4.8 %
Rwork0.239 8732 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE_FINAL_RE.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAM

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