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- PDB-3gcf: Terminal oxygenase of carbazole 1,9a-dioxygenase from Nocardioide... -

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Basic information

Entry
Database: PDB / ID: 3gcf
TitleTerminal oxygenase of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177
ComponentsTerminal oxygenase component of carbazole 1,9a-dioxygenase
KeywordsOXIDOREDUCTASE / RIESKE OXYGENASE / 2FE-2S / DIOXYGENASE / CARBAZOLE / ELECTRON TRANSFER
Function / homology
Function and homology information


dioxygenase activity / 2 iron, 2 sulfur cluster binding / 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] domain / Rieske [2Fe-2S] iron-sulphur domain ...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] domain / Rieske [2Fe-2S] iron-sulphur 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 1,9a-dioxygenase
Similarity search - Component
Biological speciesNocardioides aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsInoue, K. / Nojiri, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Specific Interactions between the ferredoxin and terminal oxygenase components of a class IIB Rieske nonheme iron oxygenase, carbazole 1,9a-dioxygenase.
Authors: Inoue, K. / Ashikawa, Y. / Umeda, T. / Abo, M. / Katsuki, J. / Usami, Y. / Noguchi, H. / Fujimoto, Z. / Terada, T. / Yamane, H. / Nojiri, H.
History
DepositionFeb 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Terminal oxygenase component of carbazole 1,9a-dioxygenase
B: Terminal oxygenase component of carbazole 1,9a-dioxygenase
C: Terminal oxygenase component of carbazole 1,9a-dioxygenase
D: Terminal oxygenase component of carbazole 1,9a-dioxygenase
E: Terminal oxygenase component of carbazole 1,9a-dioxygenase
F: Terminal oxygenase component of carbazole 1,9a-dioxygenase
G: Terminal oxygenase component of carbazole 1,9a-dioxygenase
H: Terminal oxygenase component of carbazole 1,9a-dioxygenase
I: Terminal oxygenase component of carbazole 1,9a-dioxygenase
J: Terminal oxygenase component of carbazole 1,9a-dioxygenase
K: Terminal oxygenase component of carbazole 1,9a-dioxygenase
L: Terminal oxygenase component of carbazole 1,9a-dioxygenase
M: Terminal oxygenase component of carbazole 1,9a-dioxygenase
N: Terminal oxygenase component of carbazole 1,9a-dioxygenase
O: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)675,93079
Polymers671,24915
Non-polymers4,68064
Water66,9983719
1
A: Terminal oxygenase component of carbazole 1,9a-dioxygenase
B: Terminal oxygenase component of carbazole 1,9a-dioxygenase
C: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,22817
Polymers134,2503
Non-polymers97914
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-42 kcal/mol
Surface area41560 Å2
MethodPISA
2
D: Terminal oxygenase component of carbazole 1,9a-dioxygenase
E: Terminal oxygenase component of carbazole 1,9a-dioxygenase
F: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,19316
Polymers134,2503
Non-polymers94313
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-41 kcal/mol
Surface area41630 Å2
MethodPISA
3
G: Terminal oxygenase component of carbazole 1,9a-dioxygenase
H: Terminal oxygenase component of carbazole 1,9a-dioxygenase
I: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,08713
Polymers134,2503
Non-polymers83710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-42 kcal/mol
Surface area41930 Å2
MethodPISA
4
J: Terminal oxygenase component of carbazole 1,9a-dioxygenase
K: Terminal oxygenase component of carbazole 1,9a-dioxygenase
L: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,15815
Polymers134,2503
Non-polymers90812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-42 kcal/mol
Surface area41210 Å2
MethodPISA
5
M: Terminal oxygenase component of carbazole 1,9a-dioxygenase
N: Terminal oxygenase component of carbazole 1,9a-dioxygenase
O: Terminal oxygenase component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,26418
Polymers134,2503
Non-polymers1,01415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-41 kcal/mol
Surface area41250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)280.002, 161.661, 194.665
Angle α, β, γ (deg.)90.00, 118.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44749.949 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardioides aromaticivorans (bacteria)
Strain: IC177 / Gene: carAa / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2HWI0
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3719 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 12% w/v PEG 8000, 0.4M lithium sulfate, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2006
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.91 Å / Num. obs: 319545 / % possible obs: 99.9 % / Observed criterion σ(F): 0
Reflection shellResolution: 2.3→48.91 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17508 16993 5 %RANDOM
Rwork0.17443 ---
obs0.17446 319545 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.893 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44235 0 109 3719 48063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02245585
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.311.93862085
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.41855490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5423.912340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.337157080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.93415300
X-RAY DIFFRACTIONr_chiral_restr0.0990.26450
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0236075
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.222328
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.230889
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.23526
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0020.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.2253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.31.527420
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.289244295
X-RAY DIFFRACTIONr_scbond_it2.195318165
X-RAY DIFFRACTIONr_scangle_it3.2324.517790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 1255 -
Rwork0.205 23438 -
obs--99.74 %

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