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1xd9

Crystal Structure of the Nitrogenase Fe protein Asp39Asn with MgADP bound

Method: X-RAY DIFFRACTION Dmax: 76.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nitrogenase iron protein 1

Azotobacter vinelandii

UniProt P00459

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 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

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 1XD9 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 mutation/modification 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 mutation/modification 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 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）
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 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）
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
1NIP CRYSTALLOGRAPHIC STRUCTURE OF THE NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII Deposited 1992-09-29 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）
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 conditions Resolution 2.90 Å
1RW4 Nitrogenase Fe protein l127 deletion variant Deposited 2003-12-15 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 1–272（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 experimental conditions 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 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 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 ligand/ion 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
1XDB Crystal Structure of the Nitrogenase Fe protein Asp129Glu Deposited 2004-09-05 Different mutation/modification Different ligand/ion 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 mutation/modification 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 mutation/modification 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 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）
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 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）
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 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）
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 mutation/modification 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 mutation/modification 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

SAXS profile for 1xd9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1xd9
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1xd9
Deposition date deposition_date2004-09-05
Structure title titleCrystal Structure of the Nitrogenase Fe protein Asp39Asn with MgADP bound
Keywords keywords[FeS] Cluster, Fe protein, Signal Transduction, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.78 Å
Radius of gyration Rg (electron density) rg_electron23.80 Å
Forward intensity I(0) i072347400.00
Molecular weight molecular_weight63993.0 kDa
Excluded volume excluded_volume79121 ų
Envelope volume envelope_volume93709 ų
Hydration-shell volume shell_volume31748 ų
Envelope diameter envelope_diameter78.0 Å
Shell Rg shell_rg31.90 Å
Envelope Rg envelope_rg23.81 Å
Shape Rg shape_rg23.87 Å
Total Rg total_rg24.45 Å
Total atoms total_atoms4438
Residues n_residues578
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax76.8 Å
Rg (real space) rg_real24.62 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real7.2350e+07
I(0) uncertainty (real space) i0_real_error1.0030e+06
Rg (reciprocal space) rg_reciprocal24.66 Å
I(0) (reciprocal space) i0_reciprocal72350000.0000
Solution quality estimate total_estimate0.9016
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.7 Å
Skewness Skewness skewness0.189
Kurtosis Kurtosis kurtosis-0.409
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15180000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1xd9a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.10 — Nitrogenase iron protein-like
Domain ID domain_idd1xd9b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.10 — Nitrogenase iron protein-like

CATH v4.4 (2 domains)

Domain ID domain_id1xd9A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1xd9B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)