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CRYSTALLOGRAPHIC STRUCTURE OF THE NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII

Method: X-RAY DIFFRACTION D_max: 75.3 Å Quality: EXCELLENT

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

NITROGENASE IRON PROTEIN

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–289 Chain B； UniProt 1–289	Not recorded	MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.90 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 1NIP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DE0 MODULATING THE MIDPOINT POTENTIAL OF THE [4FE-4S] CLUSTER OF THE NITROGENASE FE PROTEIN Deposited 1999-11-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Mutation：F135W Mutation：F135W	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 8.5；277 K；PEG 4000, 0.1 M TRIS HCL, 0.2 M SODIUM ACETATE, pH 8.5, SMALL TUBES, temperature 277K	Resolution 2.40 Å R-free 0.281
1FP6 THE NITROGENASE FE PROTEIN FROM AZOTOBACTER VINELANDII COMPLEXED WITH MGADP Deposited 2000-08-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Not recorded	MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8.5；298 K；PEG 4000, 0.1M Tris HCl, Sodium Acetate, Glycerol, pH 8.5, LIQUID DIFFUSION, temperature 298K	Resolution 2.15 Å R-free 0.268
1FP6 THE NITROGENASE FE PROTEIN FROM AZOTOBACTER VINELANDII COMPLEXED WITH MGADP Deposited 2000-08-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–289（289 aa） Chain D 1–289（289 aa）	Not recorded	MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8.5；298 K；PEG 4000, 0.1M Tris HCl, Sodium Acetate, Glycerol, pH 8.5, LIQUID DIFFUSION, temperature 298K	Resolution 2.15 Å R-free 0.268
1G1M ALL-FERROUS NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII Deposited 2000-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；295 K；26-29% PEG 4000, 700-900 mM NaCl, 100 mM Tris (pH 8.0), 20% glycerol, capillary microbatch method at 295 K	Resolution 2.25 Å R-free 0.288
1G20 MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASE PROTEIN COMPLEX BETWEEN LEU127DEL-FE PROTEIN AND THE MOFE PROTEIN Deposited 2000-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–289（289 aa） Chain F 1–289（289 aa） Chain G 1–289（289 aa） Chain H 1–289（289 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CFM FE-MO-S CLUSTER × 2 CA CALCIUM ION × 2 CLF FE(8)-S(7) CLUSTER × 2 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions microcapillary batch diffusion；pH 8.5；298 K；PEG 4000, sodium acetate, Tris-HCl. Ph 8.8, pH 8.5, microcapillary batch diffusion, temperature 298K	Resolution 2.20 Å R-free 0.255
1G21 MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASE PROTEIN COMPLEX BETWEEN LEU127DEL-FE PROTEIN AND THE MOFE PROTEIN Deposited 2000-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–290（290 aa） Chain F 1–290（290 aa） Chain G 1–290（290 aa） Chain H 1–290（290 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CFM FE-MO-S CLUSTER × 2 CLF FE(8)-S(7) CLUSTER × 2 CA CALCIUM ION × 2 MG MAGNESIUM ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions microcapillary batch diffusion；pH 8.5；298 K；PEG 4000, sodium acetate, Tris-HCl. Ph 8.8, pH 8.5, microcapillary batch diffusion, temperature 298K	Resolution 3.00 Å R-free 0.285
1G5P NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII Deposited 2000-11-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8；298 K；25-30% PEG 4000, 140-200 mM NA2MOO4, 100 mM TRIS-CL, PH 8.0; PROTEIN WAS IN 20% GLYCEROL, 50 mM TRIS-CL, PH 8.0, 450 mM NACL, AND 2 mM NA2S2O4 , LIQUID DIFFUSION, temperature 298K	Resolution 2.20 Å R-free 0.290
1M1Y Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein Deposited 2002-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–289（289 aa） Chain F 1–289（289 aa） Chain G 1–289（289 aa） Chain H 1–289（289 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CFM FE-MO-S CLUSTER × 2 CLF FE(8)-S(7) CLUSTER × 2 CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8；298 K；PEG 6000, NaCl, Cadaverine, Tris, pH 8.0, LIQUID DIFFUSION, temperature 298K	Resolution 3.20 Å R-free 0.329
1M1Y Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein Deposited 2002-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain M 1–289（289 aa） Chain N 1–289（289 aa） Chain O 1–289（289 aa） Chain P 1–289（289 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CFM FE-MO-S CLUSTER × 2 CLF FE(8)-S(7) CLUSTER × 2 CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8；298 K；PEG 6000, NaCl, Cadaverine, Tris, pH 8.0, LIQUID DIFFUSION, temperature 298K	Resolution 3.20 Å R-free 0.329
1N2C NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP-TETRAFLUOROALUMINATE Deposited 1997-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–289（289 aa） Chain F 1–289（289 aa） Chain G 1–289（289 aa） Chain H 1–289（289 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CFM FE-MO-S CLUSTER × 2 CA CALCIUM ION × 2 CLF FE(8)-S(7) CLUSTER × 2 MG MAGNESIUM ION × 4 ALF TETRAFLUOROALUMINATE ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；16-20% PEG 8000, 0.1 M CACODYLATE PH 6.5 AND 20-50 MM MGCL2	Resolution 3.00 Å R-free 0.238
1RW4 Nitrogenase Fe protein l127 deletion variant Deposited 2003-12-15	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–272（272 aa）	Mutation：Leu127deletion	SF4 IRON/SULFUR CLUSTER × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.272
1RW4 Nitrogenase Fe protein l127 deletion variant Deposited 2003-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–272（272 aa）	Mutation：Leu127deletion	SF4 IRON/SULFUR CLUSTER × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.272
1XCP Crystal Structure of the Nitrogenase Fe protein Phe135Trp with MgADP bound Deposited 2004-09-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Mutation：F135W Mutation：F135W	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 8.5；298 K；PEG4000, Tris HCl, sodium acetate, pH 8.5, SMALL TUBES, temperature 298K	Resolution 3.20 Å R-free 0.322
1XCP Crystal Structure of the Nitrogenase Fe protein Phe135Trp with MgADP bound Deposited 2004-09-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–289（289 aa） Chain D 1–289（289 aa）	Mutation：F135W Mutation：F135W	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 8.5；298 K；PEG4000, Tris HCl, sodium acetate, pH 8.5, SMALL TUBES, temperature 298K	Resolution 3.20 Å R-free 0.322
1XD8 Crystal Structure of the Nitrogenase Fe protein Asp39Asn Deposited 2004-09-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Mutation：D39N Mutation：D39N	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 8.5；298 K；PEG4000, Tris HCl, sodium acetate, pH 8.5, SMALL TUBES, temperature 298K	Resolution 2.70 Å R-free 0.296
1XD9 Crystal Structure of the Nitrogenase Fe protein Asp39Asn with MgADP bound Deposited 2004-09-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Mutation：D39N Mutation：D39N	MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 8.5；298 K；PEG4000, Tris HCl, sodium acetate, pH 8.5, SMALL TUBES, temperature 298K	Resolution 2.80 Å R-free 0.299
1XDB Crystal Structure of the Nitrogenase Fe protein Asp129Glu Deposited 2004-09-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Mutation：D129E Mutation：D129E	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 8.5；298 K；PEG4000, Tris HCl, sodium acetate, pH 8.5, SMALL TUBES, temperature 298K	Resolution 2.80 Å R-free 0.299
2AFH Crystal Structure of Nucleotide-Free Av2-Av1 Complex Deposited 2005-07-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–289（289 aa） Chain F 1–289（289 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CFN FE(7)-MO-S(9)-N CLUSTER × 2 PGE TRIETHYLENE GLYCOL × 8 CA CALCIUM ION × 2 NA SODIUM ION × 1 CLF FE(8)-S(7) CLUSTER × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 PG4 TETRAETHYLENE GLYCOL × 2 1PE PENTAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 3 P6G HEXAETHYLENE GLYCOL × 1 SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 10000, Tris, sodium chloride, magnesium chloride, dithionite, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298 K	Resolution 2.10 Å R-free 0.221
2AFI Crystal Structure of MgADP bound Av2-Av1 Complex Deposited 2005-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–289（289 aa） Chain F 1–289（289 aa） Chain G 1–289（289 aa） Chain H 1–289（289 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CFN FE(7)-MO-S(9)-N CLUSTER × 2 CA CALCIUM ION × 2 CLF FE(8)-S(7) CLUSTER × 2 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG8000, Sodium Chloride, Magnesium Chloride, ADP, Dithionite, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298 K	Resolution 3.10 Å R-free 0.270
2AFI Crystal Structure of MgADP bound Av2-Av1 Complex Deposited 2005-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain M 1–289（289 aa） Chain N 1–289（289 aa） Chain O 1–289（289 aa） Chain P 1–289（289 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CFN FE(7)-MO-S(9)-N CLUSTER × 2 CA CALCIUM ION × 2 CLF FE(8)-S(7) CLUSTER × 2 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG8000, Sodium Chloride, Magnesium Chloride, ADP, Dithionite, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298 K	Resolution 3.10 Å R-free 0.270
2C8V Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP Deposited 2005-12-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–126（126 aa） Chain A 128–289（162 aa）	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 2 MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；24% POLY(ETHYLENE GLYCOL), MW 4000, 0.16 M MGCL2, TRISHYDROCHLORIC ACID, PH 8.5, 20% GLYCEROL, AND 1MM SODIUM DITHIONITE	Resolution 2.50 Å R-free 0.279
2NIP NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII Deposited 1998-05-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–289（289 aa） Chain B 1–289（289 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions liquid-liquid diffusion；pH 8；PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD, USING 25-30% PEG 4000, 140-200 MM NA2MOO4, 100 MM TRIS-CL, PH 8.0; PROTEIN WAS HELD IN A BUFFER OF 20% GLYCEROL, 50 MM TRIS-CL, PH 8.0, 450 MM NACL, AND 2 MM NA2S2O4 PRIOR TO CRYSTALLIZATION., liquid-liquid diffusion	Resolution 2.20 Å R-free 0.290
4WZA Asymmetric Nucleotide Binding in the Nitrogenase Complex Deposited 2014-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–277（276 aa） Chain F 2–277（276 aa） Chain G 2–277（276 aa） Chain H 2–277（276 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 CLF FE(8)-S(7) CLUSTER × 2 FE FE (III) ION × 2 SF4 IRON/SULFUR CLUSTER × 2 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；18-22% PEG 8000, 0-50 mM NaCl, 100 mM Tris pH 8.5, 10 mM sodium dithionite, 10 mM MgCl2, 5 mM AMPPCP, 5 mM ADP	Resolution 1.90 Å R-free 0.187
4WZB Crystal Structure of MgAMPPCP-bound Av2-Av1 complex Deposited 2014-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–273（272 aa） Chain F 2–273（272 aa） Chain G 2–273（272 aa） Chain H 2–273（272 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 CLF FE(8)-S(7) CLUSTER × 2 FE2 FE (II) ION × 2 MG MAGNESIUM ION × 4 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 4 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 8000, TRIS, SODIUM CHLORIDE, MAGNESIUM CHLORIDE, DITHIONITE, AMPPCP, PH 8.5	Resolution 2.30 Å R-free 0.255
6N4J Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii Deposited 2018-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–290（289 aa） Chain B 2–290（289 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；37% PEG 3350, 0.05 M NaCl, 0.1 M Bis/Tris pH 5.5, 5 mM Ti(III) citrate	Resolution 1.95 Å R-free 0.249
6N4K Dithionite-reduced nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii Deposited 2018-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–290（289 aa） Chain B 2–290（289 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；of 40% PEG 1000, 0.2 M NaCl, 0.1 M MES/OH pH 6.5, 10% 2,2,2-trifluoroethanol, 5 mM dithionite	Resolution 1.76 Å R-free 0.213
6N4L Dithionite-reduced ADP-bound form of the nitrogenase Fe-protein from A. vinelandii Deposited 2018-11-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–290（289 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；40% PEG 400, 0.17 mM Cymal 7, 0.1 M HEPES pH 7.5, 5 mM dithionite	Resolution 1.13 Å R-free 0.157
6N4M IDS-oxidized ADP-bound form of the nitrogenase Fe-protein from A. vinelandii Deposited 2018-11-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–290（289 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；40% PEG 400, 0.17 mM Cymal 7, 0.1 M HEPES pH 7.5, 5 mM IDS	Resolution 1.58 Å R-free 0.188
7T4H Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN, with Av1) Deposited 2021-12-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal 7	Resolution 1.51 Å R-free 0.191
7TNE Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN) Deposited 2022-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.39 Å R-free 0.188
7TPN Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (11 mM KSeCN) Deposited 2022-01-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.38 Å R-free 0.197
7TPO Selenium-incorporated nitrogenase Fe-protein (Av2-Se) from A. vinelandii (1 mM KSeCN) Deposited 2022-01-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.35 Å R-free 0.203
7TPV Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii (5mM KSeCN Soaked) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 SF4 IRON/SULFUR CLUSTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7, 5 mM potassium selenocyanate	Resolution 1.49 Å R-free 0.199
7TPW Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SF4 IRON/SULFUR CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.18 Å R-free 0.158
7TPX Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.35 Å R-free 0.195
7TPY Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii (nucleotide control) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.48 Å R-free 0.194
7TPZ Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii (nucleotide control) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.71 Å R-free 0.205
7TQ0 Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN, with Av1) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.81 Å R-free 0.220
7TQ9 Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN, with Av1) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.60 Å R-free 0.194
7TQC Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.53 Å R-free 0.192
7TQE Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.59 Å R-free 0.199
7TQF Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.45 Å R-free 0.203
7TQH Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (11 mM KSeCN) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.49 Å R-free 0.204
7TQI Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (11 mM KSeCN) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.47 Å R-free 0.198
7TQJ Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (1 mM KSeCN) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.48 Å R-free 0.205
7TQK Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (1 mM KSeCN) Deposited 2022-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–290（290 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 SFS Fe4-Se4 cluster × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7	Resolution 1.48 Å R-free 0.203
8DFC CryoEM structure of the 1:1 ADP-tetrafluoroaluminate stabilized nitrogenase complex from Azotobacter vinelandii Deposited 2022-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 1–290（290 aa） Chain F 1–290（290 aa）	Not recorded	ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CLF FE(8)-S(7) CLUSTER × 2 FE FE (III) ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ALF TETRAFLUOROALUMINATE ION × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.48 Å
8DFD CryoEM structure of the 2:1 ADP-tetrafluoroaluminate stabilized nitrogenase complex from Azotobacter vinelandii Deposited 2022-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–290（290 aa） Chain F 1–290（290 aa） Chain G 1–290（290 aa） Chain H 1–290（290 aa）	Not recorded	ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 CLF FE(8)-S(7) CLUSTER × 2 FE FE (III) ION × 2 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ALF TETRAFLUOROALUMINATE ION × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.12 Å
8RHP Cryo-EM structure of the molybdenum nitrogenase complexed with iron protein (NifH) and Shethna protein II (FeSII) Deposited 2023-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain F 1–290（290 aa） Chain G 1–290（290 aa） Chain M 1–290（290 aa） Chain N 1–290（290 aa）	Not recorded	CLF FE(8)-S(7) CLUSTER × 4 HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 4 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 4 CA CALCIUM ION × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SF4 IRON/SULFUR CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
9CU0 Azotobacter vinelandii 1:1:1 MoFeP:FeP:FeSII-Complex (C1 symmetry) Deposited 2024-07-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 1–290（290 aa） Chain F 1–290（290 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 CLF FE(8)-S(7) CLUSTER × 2 FE FE (III) ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon	Resolution 3.94 Å
9CU1 Azotobacter vinelandii filamentous 2:2:1 MoFeP:FeP:FeSII-Complex (termini; C1 symmetry) Deposited 2024-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain E 1–290（290 aa） Chain F 1–290（290 aa） Chain L 1–290（290 aa） Chain M 1–290（290 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 4 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 4 CLF FE(8)-S(7) CLUSTER × 4 FE FE (III) ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 SF4 IRON/SULFUR CLUSTER × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon	Resolution 2.83 Å
9CU2 Azotobacter vinelandii filamentous 2:2:1 MoFeP:FeP:FeSII-Complex (C2 symmetry) Deposited 2024-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric	Chain E 1–290（290 aa） Chain F 1–290（290 aa） Chain L 1–290（290 aa） Chain M 1–290（290 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 4 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 4 FE FE (III) ION × 4 CLF FE(8)-S(7) CLUSTER × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4 SF4 IRON/SULFUR CLUSTER × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Samples were frozen with the SPT Labtech chameleon	Resolution 2.27 Å

47 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NIFH1_AZOVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–289； UniProt 1–289 Author chain B； PDBConstruct 1–289； UniProt 1–289

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1nip
Deposition date deposition_date	1992-09-29
Structure title title	CRYSTALLOGRAPHIC STRUCTURE OF THE NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII
Keywords keywords	IRON PROTEIN; IRON PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.51 Å
Radius of gyration Rg (electron density) rg_electron	23.52 Å
Forward intensity I(0) i0	62168800.00
Molecular weight molecular_weight	59690.0 kDa
Excluded volume excluded_volume	73905 Å³
Envelope volume envelope_volume	88350 Å³
Hydration-shell volume shell_volume	30409 Å³
Envelope diameter envelope_diameter	76.9 Å
Shell Rg shell_rg	31.37 Å
Envelope Rg envelope_rg	23.46 Å
Shape Rg shape_rg	23.60 Å
Total Rg total_rg	24.10 Å
Total atoms total_atoms	4147
Residues n_residues	570
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

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

Maximum dimension Dmax dmax	75.3 Å
Rg (real space) rg_real	24.36 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	6.2170e+07
I(0) uncertainty (real space) i0_real_error	8.4050e+05
Rg (reciprocal space) rg_reciprocal	24.40 Å
I(0) (reciprocal space) i0_reciprocal	62170000.0000
Solution quality estimate total_estimate	0.9043
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.179
Kurtosis Kurtosis kurtosis	-0.448
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14110000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NITROGENASE IRON PROTEIN
Molecular weight formula_weight	31417.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4164

AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1nipa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

Domain ID domain_id	d1nipb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

CATH v4.4 (2 domains)

Domain ID domain_id	1nipA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1nipB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (2)

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Unit-cell length a length_a	56.800 Å
Unit-cell length b length_b	92.900 Å
Unit-cell length c length_c	63.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1830
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ni/1nip/1nip.fit
pddf	/app/data/pr_computation/ni/1nip/1nip.pr.out
profile	/app/data/saxs_computation/ni/1nip/1nip.dat