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- PDB-3vmh: Oxygen-bound complex between oxygenase and ferredoxin in carbazol... -

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Basic information

Entry
Database: PDB / ID: 3vmh
TitleOxygen-bound complex between oxygenase and ferredoxin in carbazole 1,9a-dioxygenase
Components
  • Ferredoxin component of carbazole
  • Terminal oxygenase component of carbazole
KeywordsOXIDOREDUCTASE / Catalytic mechanism / Electron transfer complex / Rieske nonheme iron oxygenase system / Terminal oxygenase / Rieske-type ferredoxin / carbazole 1 / 9a-dioxygenase
Function / homology
Function and homology information


: / carbazole catabolic process / organonitrogen compound catabolic process / ferredoxin hydrogenase activity / dioxygenase activity / 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / N-terminal domain of TfIIb - #10 / 3-layer Sandwich / N-terminal domain of TfIIb ...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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / N-terminal domain of TfIIb - #10 / 3-layer Sandwich / 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 / OXYGEN MOLECULE / Terminal oxygenase component of carbazole / Ferredoxin CarAc
Similarity search - Component
Biological speciesJanthinobacterium (bacteria)
Pseudomonas resinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAshikawa, Y. / Nojiri, H.
CitationJournal: Bmc Struct.Biol. / Year: 2012
Title: Structural insight into the substrate- and dioxygenbinding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9adioxygenase
Authors: Ashikawa, Y. / Fujimoto, Z. / Usami, Y. / Inoue, K. / Noguchi, H. / Yamane, H. / Nojiri, H.
History
DepositionDec 12, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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_asym_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_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
B: Terminal oxygenase component of carbazole
C: Terminal oxygenase component of carbazole
D: Ferredoxin component of carbazole
E: Ferredoxin component of carbazole
F: Ferredoxin component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,39518
Polymers172,0766
Non-polymers1,31812
Water22,1581230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.169, 89.365, 104.995
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein Terminal oxygenase component of carbazole


Mass: 44910.738 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janthinobacterium (bacteria) / Strain: J3 / Gene: carAa / Plasmid: pEJ3AaC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84II6, EC: 1.14.12.22
#2: Protein Ferredoxin component of carbazole / / Ferredoxin component of carbazole 1 / 9a-dioxygenase


Mass: 12448.059 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas resinovorans (bacteria) / Strain: CA10 / Gene: carAc / Plasmid: pECAC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GI16, EC: 1.14.12.22

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Non-polymers , 4 types, 1242 molecules

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


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


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1230 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M ammonium acetate, 12.5% PEG 3350, 0.05M Bis-Tris, pH 5.5, 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2005
RadiationMonochromator: Rotated-inclined 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: 1.85→50 Å / Num. obs: 150169 / % possible obs: 99.9 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.363 / Num. unique all: 14838 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DE5

2de5


Resolution: 1.85→47.61 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2277080.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 7419 4.9 %RANDOM
Rwork0.196 ---
obs0.196 149887 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5427 Å2 / ksol: 0.36181 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20.53 Å2
2--0.33 Å20 Å2
3----0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.85→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11748 0 33 1230 13011
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 1214 4.9 %
Rwork0.245 23581 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3cis_peptide_AaAc_z42_1.param
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5per.paramper.top

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