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- PDB-1awd: FERREDOXIN [2FE-2S] OXIDIZED FORM FROM CHLORELLA FUSCA -

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Basic information

Entry
Database: PDB / ID: 1awd
TitleFERREDOXIN [2FE-2S] OXIDIZED FORM FROM CHLORELLA FUSCA
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / EUKARYOTIC / GREEN ALGA / ELECTRON TRANSFER / METALLOPROTEIN
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. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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 species'Chlorella' fusca (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ANOMALOUS DISPERSION TO FIND THE TWO FE ATOMS USING 2.3 ANGSTROM CU ROTATING ANODE/MULTIWIRE DATA. THE REMAINING ATOMS WERE THEN FOUND BY ROTATING A FRAGMENT (FROM ENTRY 1FXL) ABOUT THE IRON ATOMS TO MINIMIZE THE CORRELATION COEFFICIENT BETWEEN F(OBS), F(CALC). / Resolution: 1.4 Å
AuthorsSheldrick, G.M.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure determination at 1.4 A resolution of ferredoxin from the green alga Chlorella fusca
Authors: Bes, M.T. / Parisini, E. / Inda, L.A. / Saraiva, L. / Peleato, M.L. / Sheldrick, G.M.
History
DepositionOct 1, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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_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

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2022
Polymers10,0261
Non-polymers1761
Water2,270126
1
A: FERREDOXIN
hetero molecules

A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4044
Polymers20,0522
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation37_455y-1/2,x+1/2,-z+1/21
Unit cell
Length a, b, c (Å)112.440, 112.440, 112.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-178-

HOH

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Components

#1: Protein FERREDOXIN /


Mass: 10026.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 'Chlorella' fusca (plant) / Genus: Scenedesmus / References: UniProt: P56408
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growpH: 8 / Details: 1.3 M SODIUM CITRATE, 0.1 M GLYCINE AT PH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119 %protein1drop
21.1 Msodium citrate1drop
30.1 Mglycine1drop
420 mMTris-HCl1drop
51.3 Msodium citrate1reservoir
61.1 Mglycine1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1997 / Details: BENT CRYSTAL MONOCHROMATOR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 1.4→26.5 Å / Num. obs: 24157 / % possible obs: 99.9 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 25
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.42 / % possible all: 100
Reflection
*PLUS
Num. measured all: 351520
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: ANOMALOUS DISPERSION TO FIND THE TWO FE ATOMS USING 2.3 ANGSTROM CU ROTATING ANODE/MULTIWIRE DATA. THE REMAINING ATOMS WERE THEN FOUND BY ROTATING A FRAGMENT (FROM ...Method to determine structure: ANOMALOUS DISPERSION TO FIND THE TWO FE ATOMS USING 2.3 ANGSTROM CU ROTATING ANODE/MULTIWIRE DATA. THE REMAINING ATOMS WERE THEN FOUND BY ROTATING A FRAGMENT (FROM ENTRY 1FXL) ABOUT THE IRON ATOMS TO MINIMIZE THE CORRELATION COEFFICIENT BETWEEN F(OBS), F(CALC).
Resolution: 1.4→10 Å / Num. parameters: 7544 / Num. restraintsaints: 8916 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: NO RESTRAINTS ON PROSTHETIC GROUP (RESIDUE 98)
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.2%
RfactorNum. reflection% reflectionSelection details
Rfree0.1811 1202 5 %RANDOM
all0.1466 24070 --
obs0.1464 -99.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 647 / Occupancy sum non hydrogen: 796
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 0 4 126 838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.056
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.098

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