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- PDB-3gce: Ferredoxin of carbazole 1,9a-dioxygenase from Nocardioides aromat... -

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Basic information

Entry
Database: PDB / ID: 3gce
TitleFerredoxin of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177
ComponentsFerredoxin component of carbazole 1,9a-dioxygenase
KeywordsOXIDOREDUCTASE / RIESKE FERREDOXIN / 2FE-2S / DIOXYGENASE / CARBAZOLE / ELECTRON TRANSFER
Function / homology
Function and homology information


dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin component of carbazole 1,9a-dioxygenase
Similarity search - Component
Biological speciesNocardioides aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / 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 / _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: Ferredoxin component of carbazole 1,9a-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3242
Polymers13,1481
Non-polymers1761
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.116, 50.116, 82.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 13147.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardioides aromaticivorans (bacteria)
Gene: carAc / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2HWH6
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M trisodium citrate dehydrate, 2.0M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 2, 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→42.8 Å / Num. obs: 7802 / % possible obs: 98.11 % / Observed criterion σ(F): 0
Reflection shellResolution: 2→42.8 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→42.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.485 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18892 347 4.6 %RANDOM
Rwork0.17664 ---
obs0.17723 7802 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.649 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 0 4 94 876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022794
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9821088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03424.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55415118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.806155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02604
X-RAY DIFFRACTIONr_nbd_refined0.2170.2345
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2556
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.210
X-RAY DIFFRACTIONr_mcbond_it1.0771.5534
X-RAY DIFFRACTIONr_mcangle_it1.7112848
X-RAY DIFFRACTIONr_scbond_it2.7813286
X-RAY DIFFRACTIONr_scangle_it4.2014.5240
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 22 -
Rwork0.159 505 -
obs--100 %

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