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- PDB-1j7a: STRUCTURE OF THE ANABAENA FERREDOXIN D68K MUTANT -

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Basic information

Entry
Database: PDB / ID: 1j7a
TitleSTRUCTURE OF THE ANABAENA FERREDOXIN D68K MUTANT
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSPORT / electron transport / iron-sulfur / ferredoxin
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. PCC (Cyanobacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / 1.8 Å resolution
AuthorsHurley, J.K. / Weber-Main, A.M. / Stankovich, M.T. / Benning, M.M. / Thoden, J.B. / VanHooke, J.L. / Holden, H.M. / Chae, Y.K. / Xia, B. / Cheng, H. / Markley, J.L. / Martinez-Julvez, M. / Gomez-Moreno, C. / Schmeits, J.L. / Tollen, G.
CitationJournal: Biochemistry / Year: 1997
Title: Structure-function relationships in Anabaena ferredoxin: correlations between X-ray crystal structures, reduction potentials, and rate constants of electron transfer to ferredoxin:NADP+ reductase for site-specific ferredoxin mutants.
Authors: Hurley, J.K. / Weber-Main, A.M. / Stankovich, M.T. / Benning, M.M. / Thoden, J.B. / Vanhooke, J.L. / Holden, H.M. / Chae, Y.K. / Xia, B. / Cheng, H. / Markley, J.L. / Martinez-Julvez, M. / Gomez-Moreno, C. / Schmeits, J.L. / Tollin, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 16, 2001 / Release: May 23, 2001
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 23, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware_software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8962
Polyers10,7201
Non-polymers1761
Water1,802100
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)38.300, 38.300, 136.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP 32 2 1

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Components

#1: Protein/peptide FERREDOXIN I /


Mass: 10719.717 Da / Num. of mol.: 1 / Mutation: D68K / Source: (gene. exp.) Nostoc sp. PCC (Cyanobacteria) / Genus: Nostoc / Strain: 7120 / Plasmid name: PAN622 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A3C7
#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.: 100 / 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: 2.69 / Density percent sol: 54.26 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, potassium succinate, 2-methyl-2,4-pentanediol, pH 5.5, 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 mMpotassium succinate1reservoir
31 %MPD1reservoir

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Data collection

DiffractionMean temperature: 277 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Details: supper mirrors / Detector: AREA DETECTOR / Collection date: Dec 12, 1996
RadiationMonochromator: supper mirrors / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 3 Å / Number all: 10479 / Number obs: 10479 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.035 / NetI over sigmaI: 21.8 / Redundancy: 2.8 % / Percent possible obs: 86
Reflection shellRmerge I obs: 0.107 / Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / MeanI over sigI obs: 4.5 / Redundancy: 2.1 % / Percent possible all: 86
Reflection
*PLUS
Number measured all: 28370 / Percent possible obs: 89

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Processing

Software
NameClassification
TNTrefinement
FRAMBOdata collection
XDSdata scaling
TNTphasing
RefineMethod to determine structure: FOURIER SYNTHESIS / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R work: 0.174 / Highest resolution: 1.8 Å / Lowest resolution: 3 Å / Number reflection all: 10471 / Number reflection obs: 10471
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 751 / Nucleic acid: 0 / Ligand: 4 / Solvent: 100 / Total: 855
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.34
X-RAY DIFFRACTIONt_bond_d0.013
Software
*PLUS
Name: TNT / Classification: refinement
Refine
*PLUS
Sigma F: 0
Least-squares process
*PLUS
R factor R work: 0.174 / R factor obs: 0.174
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.34

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