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- PDB-1i7h: CRYSTAL STURCUTURE OF FDX -

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Basic information

Entry
Database: PDB / ID: 1i7h
TitleCRYSTAL STURCUTURE OF FDX
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / 2FE-2S
Function / homology
Function and homology information


iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / cytosol
Similarity search - Function
Ferredoxin 2Fe-2S type, proteobacteria / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding 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 ...Ferredoxin 2Fe-2S type, proteobacteria / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding 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 / 2Fe-2S ferredoxin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKakuta, Y. / Horio, T. / Takahashi, Y. / Fukuyama, K.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of Escherichia coli Fdx, an adrenodoxin-type ferredoxin involved in the assembly of iron-sulfur clusters.
Authors: Kakuta, Y. / Horio, T. / Takahashi, Y. / Fukuyama, K.
History
DepositionMar 9, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
B: FERREDOXIN
C: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5626
Polymers37,0343
Non-polymers5273
Water2,792155
1
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5212
Polymers12,3451
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5212
Polymers12,3451
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5212
Polymers12,3451
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.501, 107.501, 85.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein FERREDOXIN


Mass: 12344.811 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9R4
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
2100 mMTris-HCl1reservoirpH7.5
333 %PEG40001reservoir
45 %2-butanol1reservoir
580 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→32.6 Å / Num. obs: 155486 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 1.2 / Num. unique all: 5936 / Rsym value: 0.273 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 40083 / Num. measured all: 155486
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.57 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1247563.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 6834 9.5 %RANDOM
Rwork0.262 ---
obs0.264 71758 88.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.49 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å2-0.69 Å20 Å2
2---3.82 Å20 Å2
3---7.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 12 155 2665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 898 9.1 %
Rwork0.344 9019 -
obs--73.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FES.PARAMFES.TOP
X-RAY DIFFRACTION3WATER.PARAM
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.255 / Rfactor Rfree: 0.278
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / % reflection Rfree: 9.1 % / Rfactor Rwork: 0.344

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