2fd2

CRYSTALLOGRAPHIC ANALYSIS OF TWO SITE-DIRECTED MUTANTS OF AZOTOBACTER VINELANDII FERREDOXIN

Method: X-RAY DIFFRACTION D_max: 42.6 Å Quality: REASONABLE

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

FERREDOXIN

Azotobacter vinelandii

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–106	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2FD2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A6L T14C MUTANT OF AZOTOBACTER VINELANDII FDI Deposited 1998-02-26	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Mutation：T14C	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.8	Resolution 2.10 Å
1AXQ FERRICYANIDE OXIDIZED FDI Deposited 1997-10-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；4.8 M AMMONIUM SULFATE, 0.45 M TRIS-HCL PH 7.8	Resolution 2.10 Å
1B0T D15K/K84D MUTANT OF AZOTOBACTER VINELANDII FDI Deposited 1998-11-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–107（106 aa）	Mutation：D15K AND K84D	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.8	Resolution 2.10 Å
1B0V I40N MUTANT OF AZOTOBACTER VINELANDII FDI Deposited 1998-11-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Mutation：I40N	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.80 Å
1B0V I40N MUTANT OF AZOTOBACTER VINELANDII FDI Deposited 1998-11-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–106（106 aa）	Mutation：I40N	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.80 Å
1B0V I40N MUTANT OF AZOTOBACTER VINELANDII FDI Deposited 1998-11-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–106（106 aa）	Mutation：I40N	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.80 Å
1B0V I40N MUTANT OF AZOTOBACTER VINELANDII FDI Deposited 1998-11-12	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–106（106 aa）	Mutation：I40N	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.80 Å
1D3W Crystal structure of ferredoxin 1 d15e mutant from azotobacter vinelandii at 1.7 angstrom resolution. Deposited 1999-10-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–107（106 aa）	Mutation：D15E	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；.4M TRIS PH 7.8, 1.2 M AMMONIUM SULPHATE, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.70 Å R-free 0.247
1F5B CRYSTAL STRUCTURE OF F2H FERREDOXIN 1 MUTANT FROM AZOTOBACTER VINELANDII AT 1.75 ANGSTROM RESOLUTION Deposited 2000-06-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Mutation：F2H	F3S FE3-S4 CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；Trizma base, ammonium sulfate, potassium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K	Resolution 1.62 Å R-free 0.244
1F5C CRYSTAL STRUCTURE OF F25H FERREDOXIN 1 MUTANT FROM AZOTOBACTER VINELANDII AT 1.75 ANGSTROM RESOLUTION Deposited 2000-06-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Mutation：F25H	SO4 SULFATE ION × 1 F3S FE3-S4 CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；Trizma base, ammonium sulfate, potassium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K	Resolution 1.75 Å R-free 0.227
1FD2 SITE-DIRECTED MUTAGENESIS OF AZOTOBACTER VINELANDII FERREDOXIN I. (FE-S) CLUSTER-DRIVEN PROTEIN REARRANGEMENT Deposited 1988-12-08	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1FDA CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN AT PH 8 AND PH 6 Deposited 1993-06-29	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1FDB CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN AT PH 8 AND PH 6 Deposited 1993-06-29	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1FDD AZOTOBACTER VINELANDII FERREDOXIN I: ASPARTATE 15 FACILITATES PROTON TRANSFER TO THE REDUCED [3FE-4S] CLUSTER Deposited 1993-01-17	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1FER STRUCTURE AT PH 6.5 OF FERREDOXIN I FROM AZOTOBACTER VINELANDII AT 2.3 ANGSTROMS RESOLUTION Deposited 1992-09-02	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	F3S FE3-S4 CLUSTER × 1 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1FF2 CRYSTAL STRUCTURE OF THE C42D MUTANT OF AZOTOBACTER VINELANDII 7FE FERREDOXIN (FDI) Deposited 2000-07-24	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Mutation：C42D	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；277 K；Ammonium sulfate, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 277.0K	Resolution 2.30 Å R-free 0.269
1FRH AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SURFACE CHARGES AND THE [4FE-4S] CLUSTER REDUCTION POTENTIAL Deposited 1993-09-27	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1FRI AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SURFACE CHARGES AND THE [4FE-4S] CLUSTER REDUCTION POTENTIAL Deposited 1993-09-27	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1FRJ AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SURFACE CHARGES AND THE [4FE-4S] CLUSTER REDUCTION POTENTIAL Deposited 1993-09-27	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1FRK AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SURFACE CHARGES AND THE [4FE-4S] CLUSTER REDUCTION POTENTIAL Deposited 1993-09-27	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1FRL AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SURFACE CHARGES AND THE [4FE-4S] CLUSTER REDUCTION POTENTIAL Deposited 1993-09-27	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1FRM AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SURFACE CHARGES AND THE [4FE-4S] CLUSTER REDUCTION POTENTIAL Deposited 1993-09-27	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1FRX STRUCTURE AND PROPERTIES OF C20S FDI MUTANT Deposited 1994-07-13	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1FTC Y13C MUTANT OF AZOTOBACTER VINELANDII FDI Deposited 1997-01-08	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Mutation：Y13C Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.35 Å
1FTC Y13C MUTANT OF AZOTOBACTER VINELANDII FDI Deposited 1997-01-08	Different mutation/modification Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–106（106 aa）	Mutation：Y13C Non-standard monomer：Yes (specific site not provided by mmCIF)	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.35 Å
1G3O CRYSTAL STRUCTURE OF V19E MUTANT OF FERREDOXIN I Deposited 2000-10-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；Ammonium sulfate, tris buffer, pH 7.5, VAPOR DIFFUSION, temperature 277.0K	Resolution 1.65 Å R-free 0.265
1G6B CRYSTAL STRUCTURE OF P47S MUTANT OF FERREDOXIN I Deposited 2000-11-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；Ammonium sulfate, tris buffer, pH 7.5, VAPOR DIFFUSION, temperature 277.0K	Resolution 1.90 Å R-free 0.266
1GAO CRYSTAL STRUCTURE OF THE L44S MUTANT OF FERREDOXIN I Deposited 2000-11-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；Ammonium sulfate, Lithium sulfate, Tris buffer, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.20 Å R-free 0.286
1GAO CRYSTAL STRUCTURE OF THE L44S MUTANT OF FERREDOXIN I Deposited 2000-11-30	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；Ammonium sulfate, Lithium sulfate, Tris buffer, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.20 Å R-free 0.286
1GAO CRYSTAL STRUCTURE OF THE L44S MUTANT OF FERREDOXIN I Deposited 2000-11-30	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；Ammonium sulfate, Lithium sulfate, Tris buffer, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.20 Å R-free 0.286
1GAO CRYSTAL STRUCTURE OF THE L44S MUTANT OF FERREDOXIN I Deposited 2000-11-30	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；Ammonium sulfate, Lithium sulfate, Tris buffer, pH 7.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.20 Å R-free 0.286
1PC4 Crystal Structure of the P50A mutant of ferredoxin I at 1.65 A Resolution Deposited 2003-05-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 0–106（107 aa）	Mutation：P50A	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；298 K；Tris-HCl, Ammonium Sulfate, pH 7.4, VAPOR DIFFUSION, temperature 298K	Resolution 1.65 Å R-free 0.238
1PC5 Crystal Structure of the P50G Mutant of Ferredoxin I at 1.8 A Resolution Deposited 2003-05-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 0–106（107 aa）	Mutation：P50G	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；298 K；Tris-HCl, Ammonium Sulfate, pH 7.4, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.253
5FD1 CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN AT PH 8 AND PH 6 Deposited 1993-06-29	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
6FD1 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII LOW TEMPERATURE, 1.35 A Deposited 1997-09-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；PROTEIN CRYSTALLIZED FROM 4.8M AMMONIUM SULFATE, 0.45M TRIS-HCL, PH 7.8	Resolution 1.35 Å R-free 0.213
6FDR 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A Deposited 1998-12-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；PROTEIN CRYSTALLIZED FROM 60% SAT. AMMONIUM SULFATE, 0.4M TRIS-HCL, PH 7.8. CRYSTALS WERE SOAKED IN 5MM NA DITHIONITE, 0.15M TRIS/HCL PH 8.5 BEFORE DATA COLLECTION	Resolution 1.40 Å
7FD1 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT PH 8.5, 100 K, 1.35 A Deposited 1998-12-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；PROTEIN CRYSTALLIZED FROM 60% SAT. AMMONIUM SULFATE, 0.4M TRIS-HCL, PH 7.8 THE CRYSTALS WERE SOAKED IN 0.15M TRIS/HCL PH 8.5 BEFORE DATA COLLECTION. STARTING MODEL IN THE REFINEMENT WAS PDB ENTRY 6FD1.	Resolution 1.30 Å
7FDR 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII, NA DITHIONITE REDUCED, PH 8.5, 1.4A RESOLUTION, 100 K Deposited 1998-12-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–106（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 F3S FE3-S4 CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；PROTEIN CRYSTALLIZED FROM 60% SAT. AMMONIUM SULFATE, 0.4M TRIS-HCL, PH 7.8	Resolution 1.40 Å

31 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FER1_AZOVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–106； UniProt 1–106

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2fd2
Deposition date deposition_date	1990-08-20
Structure title title	CRYSTALLOGRAPHIC ANALYSIS OF TWO SITE-DIRECTED MUTANTS OF AZOTOBACTER VINELANDII FERREDOXIN
Keywords keywords	ELECTRON TRANSFER(IRON-SULFUR PROTEIN); ELECTRON TRANSFER(IRON-SULFUR PROTEIN)
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	13.54 Å
Radius of gyration Rg (electron density) rg_electron	12.39 Å
Forward intensity I(0) i0	3730590.00
Molecular weight molecular_weight	12648.0 kDa
Excluded volume excluded_volume	15253 Å³
Envelope volume envelope_volume	16073 Å³
Hydration-shell volume shell_volume	10878 Å³
Envelope diameter envelope_diameter	40.8 Å
Shell Rg shell_rg	18.40 Å
Envelope Rg envelope_rg	12.79 Å
Shape Rg shape_rg	12.50 Å
Total Rg total_rg	13.34 Å
Total atoms total_atoms	855
Residues n_residues	106
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	42.6 Å
Rg (real space) rg_real	13.45 Å
Rg uncertainty (real space) rg_real_error	0.17 Å
I(0) (real space) i0_real	3.7310e+06
I(0) uncertainty (real space) i0_real_error	3.2760e+04
Rg (reciprocal space) rg_reciprocal	13.46 Å
I(0) (reciprocal space) i0_reciprocal	3731000.0000
Solution quality estimate total_estimate	0.7489
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.7 Å
Skewness Skewness skewness	0.127
Kurtosis Kurtosis kurtosis	-0.395
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	504300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.994; Smooth: 0.970

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	FERREDOXIN
Molecular weight formula_weight	12027.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	885

AFVVTDNCIKCKYTDCVEVCPVDAFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEKKDPLPDAEDWDGVKGKLQHLER

来源 Source

来源生物 organism	Azotobacter vinelandii
NCBI Class编号 ncbi_taxonomy_id	354

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2fd2a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.2 — 7-Fe ferredoxin

CATH v4.4 (1 domains)

Domain ID domain_id	2fd2A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

▶

8. Citations (12)

Crystallographic analysis of two site-directed mutants of Azotobacter vinelandii ferredoxin.

J.Biol.Chem. (1991)

PMID: 1939185 PRIMARY

Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement

Proc.Natl.Acad.Sci.USA (1990)

Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution

J.Mol.Biol. (1989)

7-Iron Ferredoxin Revisited

J.Biol.Chem. (1988)

(4Fe-4S)-Cluster-Depleted Azotobacter Vinelandii Ferredoxin I. A New 3Fe Iron-Sulfur Protein

Proc.Natl.Acad.Sci.USA (1985)

Structure of Azotobacter Vinelandii 7Fe Ferredoxin. Amino Acid Sequence and Electron Density Maps of Residues

J.Biol.Chem. (1983)

Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Angstroms Resolution

J.Mol.Biol. (1982)

Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii

J.Biol.Chem. (1981)

Iron-Sulfur Clusters in Azotobacter Ferredoxin at 2.5 Angstroms Resolution

J.Biol.Chem. (1980)

Two Crystal Forms of Azotobacter Ferredoxin

J.Biol.Chem. (1979)

Structure of the Iron-Sulphur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution

Nature (1979)

Structure of the Iron-Sulfur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution

Am.Cryst.Assoc.,Abstr.Papers (Winter Meeting) (1979)

▶

Unit-cell length a length_a	55.200 Å
Unit-cell length b length_b	55.200 Å
Unit-cell length c length_c	95.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2320
R_free r_free	—

fit	/app/data/saxs_computation/fd/2fd2/2fd2.fit
pddf	/app/data/pr_computation/fd/2fd2/2fd2.pr.out
profile	/app/data/saxs_computation/fd/2fd2/2fd2.dat