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- PDB-4zhp: The crystal structure of Potato ferredoxin I with 2Fe-2S cluster -

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Basic information

Entry
Database: PDB / ID: 4zhp
TitleThe crystal structure of Potato ferredoxin I with 2Fe-2S cluster
ComponentsPotato Ferredoxin I
KeywordsELECTRON TRANSPORT / Ferredoxin 2Fe-2S cluster Electron Transfer Chloroplast
Function / homology
Function and homology information


ferredoxin metabolic process / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 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 / Ubiquitin-like (UB roll) ...Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsGrinter, R. / Josts, I. / Roszak, A.W. / Cogdell, R.J. / Walker, D.
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the bacterial plant-ferredoxin receptor FusA.
Authors: Grinter, R. / Josts, I. / Mosbahi, K. / Roszak, A.W. / Cogdell, R.J. / Bonvin, A.M. / Milner, J.J. / Kelly, S.M. / Byron, O. / Smith, B.O. / Walker, D.
History
DepositionApr 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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: Potato Ferredoxin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8402
Polymers11,6641
Non-polymers1761
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area5070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.660, 71.690, 79.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Potato Ferredoxin I


Mass: 11663.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93XJ9
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 62 %
Description: Flat plates, deep red-brown colour due to 2Fe-2S cluster
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Malic acid/MES/Tris, 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.74 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2014
RadiationMonochromator: Silicon Fliter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.46→42.7 Å / Num. obs: 5483 / % possible obs: 99.7 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.9
Reflection shellResolution: 2.46→2.52 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 4.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N58

4n58


Resolution: 2.46→42.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 14.282 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21472 270 4.9 %RANDOM
Rwork0.17688 ---
obs0.17866 5213 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.284 Å2
Baniso -1Baniso -2Baniso -3
1--5.58 Å20 Å20 Å2
2--6.34 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 2.46→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 4 17 758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019758
X-RAY DIFFRACTIONr_bond_other_d0.0010.02674
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9851030
X-RAY DIFFRACTIONr_angle_other_deg0.93131580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.78226.76534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43215122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.823151
X-RAY DIFFRACTIONr_chiral_restr0.1020.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02142
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9474.067393
X-RAY DIFFRACTIONr_mcbond_other2.9484.059392
X-RAY DIFFRACTIONr_mcangle_it4.1726.085490
X-RAY DIFFRACTIONr_mcangle_other4.1696.095491
X-RAY DIFFRACTIONr_scbond_it5.5364.76365
X-RAY DIFFRACTIONr_scbond_other5.5594.782362
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6686.889536
X-RAY DIFFRACTIONr_long_range_B_refined11.26833.472836
X-RAY DIFFRACTIONr_long_range_B_other11.26833.416833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 16 -
Rwork0.202 366 -
obs--99.48 %
Refinement TLS params.Method: refined / Origin x: 58.0562 Å / Origin y: 20.6177 Å / Origin z: 94.8137 Å
111213212223313233
T0.0619 Å2-0.0119 Å2-0.0046 Å2-0.0252 Å2-0.0011 Å2--0.0075 Å2
L5.4447 °2-0.2124 °20.7944 °2-2.7872 °2-0.6376 °2--2.1446 °2
S-0.0432 Å °-0.2318 Å °-0.0849 Å °0.1078 Å °0.0522 Å °-0.0123 Å °0.0213 Å °0.0338 Å °-0.009 Å °

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