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- PDB-7fdr: 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII, NA DITHIONITE REDUCE... -

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Basic information

Entry
Database: PDB / ID: 7fdr
Title7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII, NA DITHIONITE REDUCED, PH 8.5, 1.4A RESOLUTION, 100 K
ComponentsPROTEIN (7-FE FERREDOXIN I)
KeywordsELECTRON TRANSPORT / IRON-SULFUR
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA binding / metal ion binding
Similarity search - Function
Ferredoxin, C-terminal / : / Domain of unknown function (DUF3470) / 7Fe ferredoxin / : / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. ...Ferredoxin, C-terminal / : / Domain of unknown function (DUF3470) / 7Fe ferredoxin / : / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / IRON/SULFUR CLUSTER / Ferredoxin-1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.4 Å
AuthorsSchipke, C.G. / Goodin, D.B. / Mcree, D.E. / Stout, C.D.
CitationJournal: Biochemistry / Year: 1999
Title: Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster.
Authors: Schipke, C.G. / Goodin, D.B. / McRee, D.E. / Stout, C.D.
History
DepositionDec 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Apr 4, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _diffrn_source.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.0Sep 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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

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Assembly

Deposited unit
A: PROTEIN (7-FE FERREDOXIN I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7073
Polymers12,0601
Non-polymers6472
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.510, 54.510, 93.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROTEIN (7-FE FERREDOXIN I) / FD1


Mass: 12059.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00214
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.88 Å3/Da / Density % sol: 57.27 % / Description: ALL DATA INCLUDING NEGATIVE I'S WERE USED
Crystal growpH: 7.8
Details: PROTEIN CRYSTALLIZED FROM 60% SAT. AMMONIUM SULFATE, 0.4M TRIS-HCL, PH 7.8
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: unknown / Details: Stout, C.D., (1979) J.Biol.Chem., 254, 3598.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein11
20.5 Mpotassium phosphate11
31.2 Mammonium sulfate11
43.5 Mammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 17496 / % possible obs: 60.1 % / Redundancy: 2.28 % / Rsym value: 0.065 / Net I/σ(I): 15.4
Reflection shellResolution: 1.4→1.5 Å / Mean I/σ(I) obs: 1.1 / Rsym value: 0.31 / % possible all: 29.8
Reflection
*PLUS
Num. measured all: 66520 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.5 Å / % possible obs: 29.8 % / Rmerge(I) obs: 0.31

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Processing

Software
NameVersionClassification
TRIVIALCASEmodel building
SHELXL97refinement
X-GENdata reduction
X-GENdata scaling
TRIVIALCASEphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 6FDR

6fdr


Resolution: 1.4→100 Å / Num. parameters: 9013 / Num. restraintsaints: 10705 / σ(F): 0 / StereochEM target val spec case: FE CLUSTERS NOT RESTRAINED / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
obs0.17 -60.1 %
all-16282 -
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 776 / Occupancy sum non hydrogen: 997.5
Refinement stepCycle: LAST / Resolution: 1.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 15 142 1783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.385
X-RAY DIFFRACTIONs_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.108
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.04
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.01
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.112
X-RAY DIFFRACTIONs_approx_iso_adps0.135
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 9999 Å / σ(F): 4 / Rfactor all: 0.17 / Rfactor obs: 0.148 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.9
X-RAY DIFFRACTIONs_plane_restr0.385

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