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- PDB-1j7b: STRUCTURE OF THE ANABAENA FERREDOXIN MUTANT E94K -

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Basic information

Entry
Database: PDB / ID: 1j7b
TitleSTRUCTURE OF THE ANABAENA FERREDOXIN MUTANT E94K
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSPORT / iron sulfur / ferredoxin
Function / homology
Function and homology information


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-1
Similarity search - Component
Biological speciesNostoc sp. PCC (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
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. ...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.
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+ ...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. / ...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.
History
DepositionMay 16, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionMay 23, 2001ID: 1QOD
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)10,8822
Polymers10,7061
Non-polymers1761
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP3221

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Components

#1: Protein FERREDOXIN I /


Mass: 10705.690 Da / Num. of mol.: 1 / Mutation: E94K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC (bacteria) / Strain: 7120 / Plasmid: PAN662 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A3C7
#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.: 68 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 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
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.6 Mammonium sulfate1reservoir
250 mMpotassium succinate1reservoir
31 %MPD1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Dec 12, 1996 / Details: supper mirrors
RadiationMonochromator: supper mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 10375 / Num. obs: 10375 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 20.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 2 / % possible all: 74
Reflection
*PLUS
% possible obs: 86 % / Num. measured all: 27387

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Processing

Software
NameClassification
TNTrefinement
FRAMBOdata collection
XDSdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.183 --
all-9797 -
obs-9797 81 %
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 0 4 68 822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.275
X-RAY DIFFRACTIONt_bond_d0.012
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 0 / Rfactor all: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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