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- PDB-7buh: Reduced ferredoxin of carbazole 1,9a-dioxygenase -

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Basic information

Entry
Database: PDB / ID: 7buh
TitleReduced ferredoxin of carbazole 1,9a-dioxygenase
ComponentsFerredoxin CarAc
KeywordsOXIDOREDUCTASE / Rieske Iron-sulfur Protein
Function / homology
Function and homology information


carbazole catabolic process / ferredoxin hydrogenase activity / dioxygenase activity / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin CarAc
Similarity search - Component
Biological speciesPseudomonas resinovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsMatsuzawa, J. / Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Noda Institute for Scientific Research Japan
CitationJournal: To Be Published
Title: Reduced ferredoxin of carbazole 1,9a-dioxygenase
Authors: Matsuzawa, J. / Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H.
History
DepositionApr 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Ferredoxin CarAc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7094
Polymers12,4481
Non-polymers2613
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.045, 67.725, 45.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-615-

HOH

21A-652-

HOH

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Components

#1: Protein Ferredoxin CarAc / Carbazole 1 / 9a-dioxygenase / ferredoxin component / CARDO


Mass: 12448.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas resinovorans (bacteria) / Gene: carAc / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GI16
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
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: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Buffer: 5 mM Tris pH 7.5, Reservior: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.1, 30% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→45.45 Å / Num. obs: 9143 / % possible obs: 99.9 % / Redundancy: 26.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 29.6
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.829 / Num. unique obs: 532

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCK

1vck


Resolution: 1.79→45.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.704 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 458 5 %RANDOM
Rwork0.1572 ---
obs0.1594 8671 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.23 Å2 / Biso mean: 19.798 Å2 / Biso min: 9.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.79→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 9 106 956
Biso mean--23.35 27.76 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013897
X-RAY DIFFRACTIONr_bond_other_d0.0010.017774
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.6431225
X-RAY DIFFRACTIONr_angle_other_deg1.4141.5671801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6555120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65322.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59315126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.463154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021044
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02188
LS refinement shellResolution: 1.794→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 45 -
Rwork0.198 606 -
all-651 -
obs--98.94 %

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