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- PDB-1a70: SPINACH FERREDOXIN -

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Basic information

Entry
Database: PDB / ID: 1a70
TitleSPINACH FERREDOXIN
ComponentsFERREDOXIN
KeywordsIRON-SULFUR PROTEIN / PHOTOSYNTHESIS / ELECTRON TRANSPORT
Function / homology
Function and homology information


chloroplast stroma / 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-1, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBinda, C. / Coda, A. / Mattevi, A. / Aliverti, A. / Zanetti, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 A resolution.
Authors: Binda, C. / Coda, A. / Aliverti, A. / Zanetti, G. / Mattevi, A.
History
DepositionMar 19, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / 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 / _software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6642
Polymers10,4881
Non-polymers1761
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.000, 39.180, 83.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FERREDOXIN


Mass: 10488.470 Da / Num. of mol.: 1 / Mutation: E92K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Production host: Escherichia coli (E. coli) / References: UniProt: P00221
#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.: 81 / 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: 1.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 2.6M AMMONIUM SULPHATE IN 50MM PHOSPHATE BUFFER, PH 7.5
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
21.3 Mammonium sulfate1drop
350 mMphosphate1drop
42.6 Mammonium sulfate1reservoir
550 mMphosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 11755 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 5.1 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.112 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 2 / Rsym value: 0.305 / % possible all: 68
Reflection
*PLUS
Num. measured all: 35600
Reflection shell
*PLUS
% possible obs: 68 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Drefinement
MOSFLMdata reduction
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FRR

1frr


Resolution: 1.7→100 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: A POSTERIORI / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1090 10 %EVERY 10TH REFLECTION
Rwork0.182 ---
all0.201 11755 --
obs0.19 11755 97.6 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms732 0 4 81 817
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01962070
X-RAY DIFFRACTIONt_angle_deg2.99485590
X-RAY DIFFRACTIONt_dihedral_angle_d18.53000
X-RAY DIFFRACTIONt_incorr_chiral_ct1
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0211370
X-RAY DIFFRACTIONt_gen_planes0.02194240
X-RAY DIFFRACTIONt_it4.36202.1
X-RAY DIFFRACTIONt_nbd0.0399125
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.50
X-RAY DIFFRACTIONt_plane_restr0.021240

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