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- PDB-1ftc: Y13C MUTANT OF AZOTOBACTER VINELANDII FDI -

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Basic information

Entry
Database: PDB / ID: 1ftc
TitleY13C MUTANT OF AZOTOBACTER VINELANDII FDI
ComponentsFERREDOXIN
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 / : / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / 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 / : / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / 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 / Resolution: 2.35 Å
AuthorsKemper, M.A. / Lloyd, S.J. / Prasad, G.S. / Stout, C.D. / Fawcett, S. / Armstrong, F.A. / Burgess, B.K.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Y13C Azotobacter vinelandii ferredoxin I. A designed [Fe-S] ligand motif contains a cysteine persulfide.
Authors: Kemper, M.A. / Stout, C.D. / Lloyd, S.J. / Prasad, G.S. / Fawcett, S.E. / Armstrong, F.A. / Shen, B. / Burgess, B.K.
History
DepositionJan 8, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3586
Polymers24,0632
Non-polymers1,2954
Water00
1
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6793
Polymers12,0321
Non-polymers6472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6793
Polymers12,0321
Non-polymers6472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.300, 73.700, 45.100
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FERREDOXIN


Mass: 12031.564 Da / Num. of mol.: 2 / Mutation: Y13C
Source method: isolated from a genetically manipulated source
Details: CYS 13 MODIFIED TO A PERSULFIDE, [3FE-4S] AND [4FE-4S] CLUSTERS AS IN NATIVE PROTEIN
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Strain: JG100 / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P00214
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.5 mg/mlprotein1drop
212.5 mMTris-HCl1drop
30.63 Msodium citrate1drop
40.25 mMbeta-mercaptoethanol1drop
51.26 Msodium citrate1reservoir
60.5 mMbeta-mercaptoethanol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9116 / % possible obs: 82.5 % / Observed criterion σ(I): 0 / Redundancy: 2.76 % / Rmerge(I) obs: 0.067
Reflection
*PLUS
Highest resolution: 2.35 Å / Num. obs: 9115 / % possible obs: 85.2 % / Num. measured all: 25133
Reflection shell
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 2.43 Å / % possible obs: 32.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.35→8 Å / σ(F): 0
Details: NOTE THAT THERE ARE TWO IDENTICAL COPIES OF THE Y13C MUTANT OF FERREDOXIN IN THE ASYMMETRIC UNIT, WITH CHAIN IDENTIFIERS A AND B, AND EACH COPY HAS A MUTATED RESIDUE AT POSITION 13 ( TYR -> ...Details: NOTE THAT THERE ARE TWO IDENTICAL COPIES OF THE Y13C MUTANT OF FERREDOXIN IN THE ASYMMETRIC UNIT, WITH CHAIN IDENTIFIERS A AND B, AND EACH COPY HAS A MUTATED RESIDUE AT POSITION 13 ( TYR -> CYS ) WHICH IS FURTHER MODIFIED TO A CYSTEINE PERSULFIDE.
RfactorNum. reflection
Rwork0.216 -
obs0.216 8577
Displacement parametersBiso mean: 9.64 Å2
Refinement stepCycle: LAST / Resolution: 2.35→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 30 0 1700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49
X-RAY DIFFRACTIONx_plane_restr1.49

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