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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 / homology2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2 iron, 2 sulfur cluster binding / chloroplast ...2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2 iron, 2 sulfur cluster binding / chloroplast / electron transfer activity / metal ion binding / Ferredoxin
Function and homology information
Specimen source'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). / 1.4 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 1, 1997 / Release: Jan 14, 1998
RevisionDateData content typeGroupProviderType
1.0Jan 14, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2022
Polyers10,0261
Non-polymers1761
Water2,270126
1
A: FERREDOXIN
hetero molecules

A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4044
Polyers20,0522
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation37_455y-1/2,x+1/2,-z+1/21
Unit cell
γ
α
β
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-MI 4 3 2

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Components

#1: Protein/peptide FERREDOXIN /


Mass: 10026.017 Da / Num. of mol.: 1 / Source: (natural) 'Chlorella' fusca (plant) / Genus: Scenedesmus / References: UniProt: P56408
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 126 / Formula: H2O / Water

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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 / Density percent 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
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9091
DetectorType: MARRESEARCH / Details: BENT CRYSTAL MONOCHROMATOR / Detector: IMAGE PLATE / Collection date: Apr 26, 1997
RadiationMonochromator: GE(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionD resolution high: 1.4 Å / D resolution low: 26.5 Å / Number obs: 24157 / Rmerge I obs: 0.047 / NetI over sigmaI: 25 / Redundancy: 14.5 % / Percent possible obs: 99.9
Reflection shellRmerge I obs: 0.511 / Highest resolution: 1.4 Å / Lowest resolution: 1.5 Å / MeanI over sigI obs: 3.42 / Redundancy: 10.6 % / Percent possible all: 1
Reflection
*PLUS
Number measured all: 351520
Reflection shell
*PLUS
Percent possible obs: 1

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefineMethod 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).
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.2%
R Free selection details: RANDOM / Cross valid method: FREE R / Sigma F: 0
StereochEM target val spec case: NO RESTRAINTS ON PROSTHETIC GROUP (RESIDUE 98)
Stereochemistry target values: ENGH AND HUBER
Solvent computationSolvent model details: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228
Least-squares processR factor R free: 0.1811 / R factor all: 0.1466 / R factor obs: 0.1464 / Highest resolution: 1.4 Å / Lowest resolution: 1 Å / Number parameters: 7544 / Number reflection R free: 1202 / Number reflection all: 24070 / Number restraintsaints: 8916 / Percent reflection R free: 5 / Percent reflection obs: 99.9
Refine analyzeNumber disordered residues: 3 / Occupancy sum hydrogen: 647 / Occupancy sum non hydrogen: 796
Refine hist #LASTHighest resolution: 1.4 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 708 / Nucleic acid: 0 / Ligand: 4 / Solvent: 126 / Total: 838
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.030
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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