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- PDB-7c3a: Ferredoxin reductase in carbazole 1,9a-dioxygenase -

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Basic information

Entry
Database: PDB / ID: 7c3a
TitleFerredoxin reductase in carbazole 1,9a-dioxygenase
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
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IODIDE ION / NICKEL (II) ION / Ferredoxin reductase component of carbazole
Similarity search - Component
Biological speciesJanthinobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 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
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)114,32823
Polymers110,6503
Non-polymers3,67820
Water1,38777
1
A: Ferredoxin reductase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,29910
Polymers36,8831
Non-polymers1,4169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area15270 Å2
MethodPISA
2
B: Ferredoxin reductase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9165
Polymers36,8831
Non-polymers1,0324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area15530 Å2
MethodPISA
3
C: Ferredoxin reductase component of carbazole
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1138
Polymers36,8831
Non-polymers1,2307
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.692, 158.692, 81.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-1003-

IOD

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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, 97 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


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


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory BL-5A20.97945
SYNCHROTRONPhoton Factory AR-NW12A31.73974
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 29, 2005
ADSC QUANTUM 3152CCDJun 16, 2006
ADSC QUANTUM 2103CCDFeb 21, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979451
31.739741
ReflectionResolution: 2.6→44.1 Å / Num. obs: 32288 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3208 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
CrystalCleardata reduction
CrystalCleardata scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→35.67 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 34.2 / SU ML: 0.442 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2915 1636 5.1 %RANDOM
Rwork0.2488 ---
obs0.2509 30616 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.83 Å2 / Biso mean: 90.208 Å2 / Biso min: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2.6→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7580 0 185 77 7842
Biso mean--62.75 56.45 -
Num. residues----982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197953
X-RAY DIFFRACTIONr_bond_other_d0.0030.027523
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.99210817
X-RAY DIFFRACTIONr_angle_other_deg1.06317325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09723.061330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.746151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8131558
X-RAY DIFFRACTIONr_chiral_restr0.0680.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218854
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021795
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 128 -
Rwork0.341 2220 -
all-2348 -
obs--99.91 %
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)
13.34572.40111.12635.9828-0.13458.75110.19340.0483-0.19890.17820.01610.08370.51110.2053-0.20950.63190.05460.02670.5038-0.12560.150312.727-69.381-1.05
29.8744-1.78441.838910.0387-0.89356.1119-0.27160.56521.4561-0.105-0.0818-1.0991-0.07270.46720.35330.6507-0.0360.04070.5576-0.04440.325820.108-48.6659.169
312.48130.7248-1.91435.7578-1.9117.0619-0.2974-1.1831-0.2070.946-0.2249-0.95940.13430.53040.52231.24730.2424-0.01120.93570.03030.186416.213-58.50328.677
43.5005-2.05540.04957.1068-1.15174.0863-0.09830.2001-0.485-0.0072-0.06830.04350.0327-0.41590.16660.5552-0.0778-0.22680.644-0.10040.40436.261-44.488-22.007
57.55712.50761.98.15970.89474.12880.2911-0.1922-0.61320.6436-0.1103-0.9640.54210.3111-0.18080.61810.005-0.29380.6838-0.08130.695226.565-31.383-18.36
63.0913-0.5443-0.15014.24220.94313.84220.0482-0.00380.61980.0850.0702-0.2821-0.38460.4516-0.11830.7604-0.054-0.14490.8543-0.06070.947514.549-12.332-19.578
715.12250.78-1.9663.23970.11935-0.01370.97250.1552-0.67720.36360.33730.2475-0.1205-0.34990.7948-0.0692-0.16330.6365-0.06330.090731.836-65.582-27.472
89.63723.25911.02298.23080.1015.44630.0413-0.3090.87520.33680.090.4102-0.0003-0.0731-0.13130.4866-0.0143-0.00260.5437-0.0140.090845.798-57.789-10.021
98.99351.1224-0.31098.98111.11642.4043-0.24230.7345-0.3372-0.70180.403-0.9378-0.17910.078-0.16070.635-0.07490.2130.8064-0.09950.292464.234-59.786-22.329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 96
2X-RAY DIFFRACTION2A97 - 196
3X-RAY DIFFRACTION3A197 - 329
4X-RAY DIFFRACTION4B-3 - 96
5X-RAY DIFFRACTION5B97 - 196
6X-RAY DIFFRACTION6B197 - 328
7X-RAY DIFFRACTION7C-4 - 96
8X-RAY DIFFRACTION8C97 - 196
9X-RAY DIFFRACTION9C197 - 329

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