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- PDB-1czp: ANABAENA PCC7119 [2FE-2S] FERREDOXIN IN THE REDUCED AND OXIXIZED ... -

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Basic information

Entry
Database: PDB / ID: 1czp
TitleANABAENA PCC7119 [2FE-2S] FERREDOXIN IN THE REDUCED AND OXIXIZED STATE AT 1.17 A
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSPORT / [2FE-2S] PROTEIN / CRYSTAL REDUCED WITH DITHIONITE
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 / electron transfer activity ...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 / electron transfer activity / metal ion binding / Ferredoxin-1
Function and homology information
Specimen sourceNostoc sp. (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.17 Å resolution
AuthorsMorales, R. / Charon, M.H. / Frey, M.
CitationJournal: Biochemistry / Year: 1999
Title: Refined X-ray structures of the oxidized, at 1.3 A, and reduced, at 1.17 A, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes.
Authors: Morales, R. / Charon, M.H. / Hudry-Clergeon, G. / Petillot, Y. / Norager, S. / Medina, M. / Frey, M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 6, 1999 / Release: Jan 14, 2000
RevisionDateData content typeGroupProviderType
1.0Jan 14, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN I
B: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7634
Polyers21,4112
Non-polymers3522
Water6,648369
1
A: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8812
Polyers10,7061
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8812
Polyers10,7061
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)37.220, 37.370, 146.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide FERREDOXIN I /


Mass: 10705.624 Da / Num. of mol.: 2 / Source: (natural) Nostoc sp. (Cyanobacteria) / Genus: Nostoc / Strain: PCC 7119 / References: UniProt: P0A3C8
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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 / Density percent sol: 48.32 %
Description: REDUCED CRYSTAL WITH SODIUM DITHIONITE IN ANAEROBIC ATMOSPHERE
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 MM SODIUM SUCCINATE PH 5.5, 2.6 M AMMONIUM SULFATE, 1% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temp: 4 ℃
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
12.6 Mammonium sulfate1reservoir
250 mMsodium succinate1reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.75
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 12.7 Å2 / D resolution high: 1.17 Å / D resolution low: 3 Å / Number all: 67690 / Number obs: 67690 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.033 / NetI over sigmaI: 12 / Redundancy: 4.3 % / Percent possible obs: 95.5
Reflection shellRmerge I obs: 0.111 / Highest resolution: 1.17 Å / Lowest resolution: 1.22 Å / MeanI over sigI obs: 6.1 / Redundancy: 2.8 % / Percent possible all: 89.3
Reflection
*PLUS
Number obs: 67611 / Rmerge I obs: 0.037
Reflection shell
*PLUS
Percent possible obs: 89.3

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Processing

Software
NameVersionClassification
AMoREphasing
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FXA
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995) 53-56. ANISOTROPIC REFINEMENT REDUCED R-FREE (NO CUTOFF) BY 4 %
R Free selection details: RANDOM / Cross valid method: FREE R / Sigma F: 0 / Sigma I: 0
StereochEM target val spec case: [2FE-2S] CLUSTERS NOT RESTRAINED
Stereochemistry target values: ENGH & HUBER
Solvent computationSolvent model details: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228
Least-squares processR factor R free: 0.1837 / R factor R work: 0.14 / R factor all: 0.143 / R factor obs: 0.143 / Highest resolution: 1.17 Å / Lowest resolution: 15 Å / Number parameters: 1756 / Number reflection R free: 6799 / Number reflection all: 67145 / Number reflection obs: 60346 / Number restraintsaints: 2142 / Percent reflection R free: 1 / Percent reflection obs: 86.1
Refine analyzeNumber disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1878
Refine hist #LASTHighest resolution: 1.17 Å / Lowest resolution: 15 Å
Number of atoms included #LASTProtein: 1500 / Nucleic acid: 0 / Ligand: 8 / Solvent: 369 / Total: 1877
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0.00
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.00
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.09
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg0.029

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