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- PDB-4itk: The structure of C.reinhardtii Ferredoxin 2 -

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Basic information

Entry
Database: PDB / ID: 4itk
TitleThe structure of C.reinhardtii Ferredoxin 2
ComponentsApoferredoxin
KeywordsELECTRON TRANSPORT / ferredoxin fold / FERREDOXIN / iron-sulfur
Function / homology
Function and homology information


chloroplast / 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 speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Photosyn. Res. / Year: 2016
Title: Crystal structure and biochemical characterization of Chlamydomonas FDX2 reveal two residues that, when mutated, partially confer FDX2 the redox potential and catalytic properties of FDX1.
Authors: Boehm, M. / Alahuhta, M. / Mulder, D.W. / Peden, E.A. / Long, H. / Brunecky, R. / Lunin, V.V. / King, P.W. / Ghirardi, M.L. / Dubini, A.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / 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
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7503
Polymers11,4821
Non-polymers2682
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.429, 26.458, 31.016
Angle α, β, γ (deg.)102.56, 104.35, 100.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Apoferredoxin


Mass: 11481.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: FDX2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2HZ25
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 1.67 Å3/Da / Density % sol: 26.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 3.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 31, 2012
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.18→25 Å / Num. all: 24232 / Num. obs: 24232 / % possible obs: 99.4 % / Redundancy: 6.06 % / Rsym value: 0.0838
Reflection shellResolution: 1.18→1.28 Å / Redundancy: 2.31 % / Mean I/σ(I) obs: 2.59 / Num. unique all: 5195 / Rsym value: 0.2948 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MrBump/Molrepmodel building
REFMAC5.7.0032refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
MrBump/Molrepphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RFK
Resolution: 1.18→25 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.438 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14745 1132 4.9 %RANDOM
Rwork0.10855 ---
obs0.11049 22057 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0.35 Å2-0.17 Å2
2--0.38 Å2-0.18 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.18→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 10 142 941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.019982
X-RAY DIFFRACTIONr_bond_other_d0.0020.02911
X-RAY DIFFRACTIONr_angle_refined_deg2.4972.0041339
X-RAY DIFFRACTIONr_angle_other_deg1.30832152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31227.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48815188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.28151
X-RAY DIFFRACTIONr_chiral_restr0.1380.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021175
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02190
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr10.56531893
X-RAY DIFFRACTIONr_sphericity_free31.767532
X-RAY DIFFRACTIONr_sphericity_bonded14.34751994
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 78 -
Rwork0.246 1423 -
obs--81.62 %

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