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- PDB-7c3b: Ferredoxin reductase in carbazole 1,9a-dioxygenase (FAD apo form) -

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Basic information

Entry
Database: PDB / ID: 7c3b
TitleFerredoxin reductase in carbazole 1,9a-dioxygenase (FAD apo form)
ComponentsFerredoxin reductase component of carbazole
KeywordsOXIDOREDUCTASE / Rieske non-heme iron oxygenase / NAD(P)H:ferredoxin oxidoreductase / ferredoxin / electron transfer / carbazole
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding ...Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
ACETATE ION / FE2/S2 (INORGANIC) CLUSTER / IODIDE ION / NICKEL (II) ION / Ferredoxin reductase component of carbazole
Similarity search - Component
Biological speciesJanthinobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAshikawa, Y. / Fujimoto, Z. / Nojiri, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17380052 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structure of the ferredoxin reductase component of carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3.
Authors: Ashikawa, Y. / Fujimoto, Z. / Inoue, K. / Yamane, H. / Nojiri, H.
History
DepositionMay 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 29, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin reductase component of carbazole
B: Ferredoxin reductase component of carbazole
C: Ferredoxin reductase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,31429
Polymers110,6503
Non-polymers1,66426
Water3,063170
1
A: Ferredoxin reductase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,49311
Polymers36,8831
Non-polymers61010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-17 kcal/mol
Surface area15390 Å2
MethodPISA
2
B: Ferredoxin reductase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3999
Polymers36,8831
Non-polymers5158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area14020 Å2
MethodPISA
3
C: Ferredoxin reductase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4229
Polymers36,8831
Non-polymers5398
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-17 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.924, 161.924, 79.606
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Ferredoxin reductase component of carbazole


Mass: 36883.332 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janthinobacterium sp. (strain J3) (bacteria)
Strain: J3 / Gene: carAd / Plasmid: pEJ3NAd / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84II0

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Non-polymers , 6 types, 196 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.16 mM calcium acetate or magnesium acetate, 8-12%(w/v) PEG 8000, 0.2 M sodium iodide, 0.08 M MES
PH range: 6.5-6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→44.91 Å / Num. obs: 41796 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3 / Num. unique obs: 4118 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.452 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.512 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 2106 5 %RANDOM
Rwork0.2274 ---
obs0.23 39641 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.42 Å2 / Biso mean: 70.245 Å2 / Biso min: 32.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 2.4→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7449 0 38 170 7657
Biso mean--45.39 45.61 -
Num. residues----964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197645
X-RAY DIFFRACTIONr_bond_other_d0.0030.027322
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.96610358
X-RAY DIFFRACTIONr_angle_other_deg1.028316849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69222.985325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.284151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2331557
X-RAY DIFFRACTIONr_chiral_restr0.0760.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218586
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021745
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 168 -
Rwork0.322 2757 -
all-2925 -
obs--96.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9985-0.69360.53663.48011.18017.16250.20.0382-0.0228-0.2134-0.0167-0.060.11240.1806-0.18330.1023-0.0024-0.01210.0828-0.05730.044917.107-70.412-5.52
25.12692.15610.77646.96160.71724.96880.09350.38050.3814-0.3677-0.1132-0.3753-0.52760.51020.01980.2535-0.02510.070.12680.01240.11920.3-50.9947.689
35.5756-0.2586-1.66593.2929-0.16846.1157-0.0283-0.7984-0.15110.5430.0249-0.3264-0.14790.66450.00340.1739-0.035-0.02340.277-0.05440.081319.531-63.38125.492
44.1886-1.65210.84065.9511-0.61463.77910.02110.045-0.7762-0.16350.12070.51360.2718-0.1604-0.14180.126-0.0762-0.12050.2181-0.00410.34799.8-44.431-24.397
58.8409-0.65791.58744.9811.18034.5492-0.1602-0.3641-0.47580.26120.0998-0.42490.29760.26810.06040.0915-0.0551-0.06160.31280.01740.244629.05-30.891-18.974
66.4742-1.4532-0.83124.49430.15024.4201-0.0682-0.3151.13710.16270.1265-0.2477-0.47360.2601-0.05830.1933-0.079-0.10940.3011-0.04690.334314.117-14.888-18.054
77.6483-0.8837-1.15385.03451.11782.43050.14590.8716-0.1222-0.9334-0.42610.5737-0.2677-0.54840.28020.32270.1213-0.14680.6548-0.12450.112236.734-63.035-30.991
85.87030.98531.13115.47231.57486.8178-0.0285-0.19330.30570.1259-0.08430.4963-0.5009-0.71620.11280.13730.04220.01210.3605-0.01240.05448.901-59.137-11.112
95.97810.01060.05272.95210.97044.2719-0.0229-0.0890.0497-0.09020.0287-0.2226-0.24330.1398-0.00580.20360.01670.04320.19760.01360.027367.885-59.664-22.444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 96
2X-RAY DIFFRACTION2A97 - 196
3X-RAY DIFFRACTION3A197 - 329
4X-RAY DIFFRACTION4B-3 - 96
5X-RAY DIFFRACTION5B97 - 196
6X-RAY DIFFRACTION6B197 - 329
7X-RAY DIFFRACTION7C-4 - 96
8X-RAY DIFFRACTION8C97 - 196
9X-RAY DIFFRACTION9C197 - 329

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