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- PDB-3av8: Refined Structure of Plant-type [2Fe-2S] Ferredoxin I from Aphano... -

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Basic information

Entry
Database: PDB / ID: 3av8
TitleRefined Structure of Plant-type [2Fe-2S] Ferredoxin I from Aphanothece sacrum at 1.46 A Resolution
ComponentsFerredoxin-1
KeywordsELECTRON TRANSPORT / Beta-grasp / Redox Protein
Function / homology
Function and homology information


electron transport chain / 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. / 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) ...Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 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 / Ferredoxin-1
Similarity search - Component
Biological speciesAphanothece sacrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsKameda, H. / Hirabayashi, K. / Wada, K. / Fukuyama, K.
CitationJournal: Plos One / Year: 2011
Title: Mapping of protein-protein interaction sites in the plant-type [2Fe-2S] ferredoxin.
Authors: Kameda, H. / Hirabayashi, K. / Wada, K. / Fukuyama, K.
History
DepositionFeb 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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

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Assembly

Deposited unit
A: Ferredoxin-1
B: Ferredoxin-1
C: Ferredoxin-1
D: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,49310
Polymers41,5984
Non-polymers8956
Water8,737485
1
A: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5752
Polymers10,3991
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6713
Polymers10,3991
Non-polymers2722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6713
Polymers10,3991
Non-polymers2722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5752
Polymers10,3991
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.027, 92.027, 46.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Ferredoxin-1 / Ferredoxin I


Mass: 10399.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aphanothece sacrum (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: P00250*PLUS
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5
Details: 70-80% ammonium sulfate, 0.1M TRIS, 0.7M sodium chloride, pH 7.5, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 15, 2010
RadiationMonochromator: A Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→25 Å / Num. obs: 66810 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.05
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 5.5 % / Rsym value: 0.383 / % possible all: 99.6

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Processing

Software
NameClassification
BSSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FXI

1fxi


Resolution: 1.46→24.64 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 269412.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3215 5.1 %RANDOM
Rwork0.187 ---
all0.196 63524 --
obs0.187 63524 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.1651 Å2 / ksol: 0.405467 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--5.52 Å20 Å20 Å2
2---5.52 Å20 Å2
3---11.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.46→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 26 485 3415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.027
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.8
X-RAY DIFFRACTIONc_mcbond_it4.11.5
X-RAY DIFFRACTIONc_mcangle_it5.082
X-RAY DIFFRACTIONc_scbond_it6.542
X-RAY DIFFRACTIONc_scangle_it7.782.5
LS refinement shellResolution: 1.46→1.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 466 4.8 %
Rwork0.281 9180 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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