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- PDB-9i2a: FdC of Rhodobacter capsulatus -

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Basic information

Entry
Database: PDB / ID: 9i2a
TitleFdC of Rhodobacter capsulatus
ComponentsFerredoxin-4
KeywordsELECTRON TRANSPORT / Ferredoxin / Fdc / Fdx / Rhodobacter / Nitrogenase / Nitrogen / Fixation / Anaerobe / Anoxic / FeS / Iron / Sulfur
Function / homology
Function and homology information


nitrogen fixation / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin-4
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPfister, P. / Addison, H.G. / Erb, T.J. / Rebelein, J.G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Chemistry / Year: 2025
Title: Two Key Ferredoxins for Nitrogen Fixation Have Different Specificities and Biophysical Properties.
Authors: Addison, H. / Pfister, P. / Lago-Maciel, A. / Erb, T.J. / Pierik, A.J. / Rebelein, J.G.
History
DepositionJan 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin-4
B: Ferredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9254
Polymers22,5742
Non-polymers3522
Water1,820101
1
A: Ferredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4632
Polymers11,2871
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4632
Polymers11,2871
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.870, 45.830, 85.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ferredoxin-4 / Ferredoxin IV / FdIV / Ferredoxin / plant-type


Mass: 11286.864 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-Ai / References: UniProt: D5ARY7
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0,1 M Tris 8 20 % w/v SOKALAN PA 25 CL in anoxic environment

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryojet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.36
ReflectionResolution: 1.6→24.17 Å / Num. obs: 24473 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Net I/σ(I): 15
Reflection shellResolution: 1.6→1.69 Å / Num. unique obs: 3519 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.34 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1842 1988 9.75 %
Rwork0.1773 --
obs0.1894 20381 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 101 1528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041438
X-RAY DIFFRACTIONf_angle_d0.551935
X-RAY DIFFRACTIONf_dihedral_angle_d10.95552
X-RAY DIFFRACTIONf_chiral_restr0.042231
X-RAY DIFFRACTIONf_plane_restr0.004253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.23351390.27491248X-RAY DIFFRACTION90
1.74-1.790.2681380.2491307X-RAY DIFFRACTION90
1.79-1.840.22431400.23481304X-RAY DIFFRACTION90
1.84-1.90.2181420.23171290X-RAY DIFFRACTION90
1.9-1.970.24191380.21131283X-RAY DIFFRACTION90
1.97-2.050.20591390.22341291X-RAY DIFFRACTION90
2.05-2.140.19081440.21571314X-RAY DIFFRACTION90
2.14-2.250.24461410.20431294X-RAY DIFFRACTION90
2.25-2.40.19191430.20771313X-RAY DIFFRACTION90
2.4-2.580.20681410.20471318X-RAY DIFFRACTION90
2.58-2.840.2081350.19691336X-RAY DIFFRACTION91
2.84-3.250.23411480.17391325X-RAY DIFFRACTION90
3.25-4.080.16131460.1691347X-RAY DIFFRACTION90
4.09-19.340.15021540.14721423X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 4.6108 Å / Origin y: -1.4827 Å / Origin z: -4.5526 Å
111213212223313233
T0.1785 Å2-0.0078 Å2-0.0053 Å2-0.2255 Å20.0089 Å2--0.0673 Å2
L0.1959 °2-0.1083 °2-0.016 °2-0.5381 °20.6364 °2--1.1773 °2
S0.024 Å °-0.0262 Å °0.0056 Å °-0.0198 Å °-0.0174 Å °0.0189 Å °-0.0212 Å °-0.0587 Å °0.0035 Å °
Refinement TLS groupSelection details: all

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