8p8g

Nitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G

Method: X-RAY DIFFRACTION D_max: 124.1 Å Quality: GOOD

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

Nitrogenase protein alpha chain

Azotobacter vinelandii DJ

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 3–492 Chain C； UniProt 3–492	Not recorded	Nitrogenase molybdenum-iron protein beta chain × 2 （C1DGZ8） EDO 1,2-ETHANEDIOL × 35 CL CHLORIDE ION × 2 HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 DIO 1,4-DIETHYLENE DIOXIDE × 2 GOL GLYCEROL × 1 1CL FE(8)-S(7) CLUSTER, OXIDIZED × 2 CLF FE(8)-S(7) CLUSTER × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293.15 K；The beta-D353G/D357G MoFe-protein was crystallized anaerobically at 17.5 mg/mL under 100% N2 atmosphere. The protein was spotted as a sitting drop to 96-Well MRC 2-Drop polystyrene Crystallization Plates (SWISSCI) containing 90 uL of crystallization solution in the reservoir. Each drop contained 0.5 uL of protein sample and 0.5 uL of crystallization solution. Crystals were obtained in the crystallization solution containing 10 % w/v Polyethylene glycol 10,000; 2 % v/v 1,4-Dioxane; 100 mM tri-Sodium citrate; pH 5.6, and 1 mM polyoxotungstate [TeW6O24]6- (TEW). Sealed plates were stored inside a Coy anaerobic chamber filled with an atmosphere of N2:H2 97:3 at 20 C. Crystals were soaked in the crystallization solution supplemented with 30% v/v ethylene glycol for a few seconds before freezing in liquid nitrogen.	Resolution 1.55 Å R-free 0.187

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 8P8G	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8BTS Nitrogenase MoFe protein from A. vinelandii alpha double mutant C45A/L158C Deposited 2022-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 3–492（490 aa） Chain C 3–492（490 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 GOL GLYCEROL × 10 SO4 SULFATE ION × 5 1CL FE(8)-S(7) CLUSTER, OXIDIZED × 2 FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；The purified enzyme in 50 mM Tris/HCl pH 8.0, 300 mM NaCl, 2 mM dithionite was crystallized at 8 mg.ml-1. Crystallization was performed anaerobically in a tent containing 100 % N2 atmosphere. Crystals were obtained by initial screening at 20 degree Celsius on 96-Well MRC 2-drop crystallization plates in polystyrene (SWISSCI) containing 90 ul of crystallization solution in the reservoir. The protein sample (0.5 ul) was mixed with 0.5 ul reservoir solution. The reservoir solution contained 25 % w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS at pH 5.5, and 200 mM Lithium sulfate. The plate was then incubated in a Coy tent (N2/H2, 97:3) at 20 degree Celsius. Crystals appeared after a few weeks and were soaked in the crystallization solution supplemented with 15 % v/v glycerol as a cryo-protectant before being frozen in liquid nitrogen.	Resolution 3.03 Å R-free 0.223
8BTS Nitrogenase MoFe protein from A. vinelandii alpha double mutant C45A/L158C Deposited 2022-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 3–492（490 aa） Chain J 3–492（490 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 5 1CL FE(8)-S(7) CLUSTER, OXIDIZED × 2 FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；The purified enzyme in 50 mM Tris/HCl pH 8.0, 300 mM NaCl, 2 mM dithionite was crystallized at 8 mg.ml-1. Crystallization was performed anaerobically in a tent containing 100 % N2 atmosphere. Crystals were obtained by initial screening at 20 degree Celsius on 96-Well MRC 2-drop crystallization plates in polystyrene (SWISSCI) containing 90 ul of crystallization solution in the reservoir. The protein sample (0.5 ul) was mixed with 0.5 ul reservoir solution. The reservoir solution contained 25 % w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS at pH 5.5, and 200 mM Lithium sulfate. The plate was then incubated in a Coy tent (N2/H2, 97:3) at 20 degree Celsius. Crystals appeared after a few weeks and were soaked in the crystallization solution supplemented with 15 % v/v glycerol as a cryo-protectant before being frozen in liquid nitrogen.	Resolution 3.03 Å R-free 0.223

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C1DGZ7_AZOVD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–500； UniProt 3–492 Author chain C； PDBConstruct 11–500； UniProt 3–492

Nitrogenase molybdenum-iron protein beta chain

Azotobacter vinelandii DJ

UniProt C1DGZ8

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–523 Chain D； UniProt 1–523	Mutation：D353G and D357G	Nitrogenase protein alpha chain × 2 （C1DGZ7） EDO 1,2-ETHANEDIOL × 35 CL CHLORIDE ION × 2 HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 DIO 1,4-DIETHYLENE DIOXIDE × 2 GOL GLYCEROL × 1 1CL FE(8)-S(7) CLUSTER, OXIDIZED × 2 CLF FE(8)-S(7) CLUSTER × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293.15 K；The beta-D353G/D357G MoFe-protein was crystallized anaerobically at 17.5 mg/mL under 100% N2 atmosphere. The protein was spotted as a sitting drop to 96-Well MRC 2-Drop polystyrene Crystallization Plates (SWISSCI) containing 90 uL of crystallization solution in the reservoir. Each drop contained 0.5 uL of protein sample and 0.5 uL of crystallization solution. Crystals were obtained in the crystallization solution containing 10 % w/v Polyethylene glycol 10,000; 2 % v/v 1,4-Dioxane; 100 mM tri-Sodium citrate; pH 5.6, and 1 mM polyoxotungstate [TeW6O24]6- (TEW). Sealed plates were stored inside a Coy anaerobic chamber filled with an atmosphere of N2:H2 97:3 at 20 C. Crystals were soaked in the crystallization solution supplemented with 30% v/v ethylene glycol for a few seconds before freezing in liquid nitrogen.	Resolution 1.55 Å R-free 0.187

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8P8G	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7MCI MoFe protein from Azotobacter vinelandii with a sulfur-replenished cofactor Deposited 2021-04-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–523（523 aa） Chain D 1–523（523 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 H2S HYDROSULFURIC ACID × 2 MO MOLYBDENUM ATOM × 6 CLF FE(8)-S(7) CLUSTER × 2 GOL GLYCEROL × 11 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1M CHC (pH5), 0.16M ammonium acetate, 25.6% (v/v) glycerol, 2% MPD, 0.1M CsCl, 1mM Dithiothreitol, 5mM Eu-EGTA, 16% PEG smear high	Resolution 1.65 Å R-free 0.195
7UT6 C1 symmetric cryoEM structure of Azotobacter vinelandii MoFeP under non-turnover conditions Deposited 2022-04-26	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–523（523 aa） Chain D 1–523（523 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 FE FE (III) ION × 2 CLF FE(8)-S(7) CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	Resolution 1.91 Å
7UT7 C2 symmetric cryoEM structure of Azotobacter vinelandii MoFeP under non-turnover conditions Deposited 2022-04-26	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–523（523 aa） Chain D 1–523（523 aa）	Not recorded	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 FE FE (III) ION × 2 CLF FE(8)-S(7) CLUSTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	Resolution 1.91 Å
7UT8 CryoEM structure of Azotobacter vinelandii nitrogenase complex (1:1 FeP:MoFeP, ATP-bound) during catalytic N2 reduction Deposited 2022-04-26	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 B 1–523（523 aa） Chain D 1–523（523 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 × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	Resolution 2.43 Å
7UT9 CryoEM structure of Azotobacter vinelandii nitrogenase complex (1:1 FeP:MoFeP, ADP/ATP-bound) during catalytic N2 reduction Deposited 2022-04-26	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 B 1–523（523 aa） Chain D 1–523（523 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 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	Resolution 2.44 Å
7UTA CryoEM structure of Azotobacter vinelandii nitrogenase complex (2:1 FeP:MoFeP) inhibited by BeFx during catalytic N2 reduction Deposited 2022-04-26	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 B 1–523（523 aa） Chain D 1–523（523 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 × 4 0BE BERYLLIUM × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	Resolution 2.40 Å
8DPN CryoEM structure of Azotobacter vinelandii nitrogenase MoFeP during catalytic N2 reduction Deposited 2022-07-15	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–523（523 aa） Chain D 1–523（523 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	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	Resolution 2.49 Å
8E3T Gallium-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation Deposited 2022-08-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–523（523 aa） Chain D 1–523（523 aa）	Mutation：S188A Mutation：S188A	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 UFF FE(7)-S(7) CLUSTER × 2 FE FE (III) ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% PEG 8000, 100 mM Tris pH 8.5, 500 mM NaCl, 10 mM dithionite	Resolution 2.20 Å R-free 0.243
8E3U Nickel-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation Deposited 2022-08-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–523（523 aa） Chain D 1–523（523 aa）	Mutation：S188A Mutation：S188A	UFF FE(7)-S(7) CLUSTER × 2 HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 FE FE (III) ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.25；293 K；18% PEG 8000, 100 mM Tris pH 8.25, 500 mM NaCl, 10 mM dithionite	Resolution 1.99 Å R-free 0.253
8E3V Cobalt-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation Deposited 2022-08-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–523（523 aa） Chain D 1–523（523 aa）	Mutation：S188A Mutation：S188A	HCA 3-HYDROXY-3-CARBOXY-ADIPIC ACID × 2 ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 FE FE (III) ION × 2 CLF FE(8)-S(7) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.75；293 K；20% PEG 8000, 100 mM Tris pH 7.75, 500 mM NaCl, 10 mM dithionite	Resolution 2.00 Å R-free 0.208
8ENN Homocitrate-deficient nitrogenase MoFe-protein from Azotobacter vinelandii nifV knockout Deposited 2022-09-30	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 2–523（522 aa） Chain D 2–523（522 aa）	Not recorded	ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 CLF FE(8)-S(7) CLUSTER × 2 1N7 CHAPSO × 2 FE FE (III) ION × 2 CIT CITRIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.58 Å
8ENO Homocitrate-deficient nitrogenase MoFe-protein from A. vinelandii nifV knockout in complex with NafT Deposited 2022-09-30	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 × 5 PDB declaration: pentameric	Chain B 2–523（522 aa） Chain D 2–523（522 aa）	Not recorded	ICS iron-sulfur-molybdenum cluster with interstitial carbon × 2 CIT CITRIC ACID × 1 CLF FE(8)-S(7) CLUSTER × 2 1N7 CHAPSO × 2 FE FE (III) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.71 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C1DGZ8_AZOVD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–523； UniProt 1–523 Author chain D； PDBConstruct 1–523； UniProt 1–523

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	8p8g
Deposition date deposition_date	2023-06-01
最后修订 last_revision	2023-12-13
Structure title title	Nitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G
Keywords keywords	Molybdenum nitrogenase, N2-fixation, FeMocofactor, metal binding site, P cluster, NH3 production, OXIDOREDUCTASE; OXIDOREDUCTASE
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	38.46 Å
Radius of gyration Rg (electron density) rg_electron	37.84 Å
Forward intensity I(0) i0	811038000.00
Molecular weight molecular_weight	232020.0 kDa
Excluded volume excluded_volume	288920 Å³
Envelope volume envelope_volume	333750 Å³
Hydration-shell volume shell_volume	70028 Å³
Envelope diameter envelope_diameter	125.6 Å
Shell Rg shell_rg	46.28 Å
Envelope Rg envelope_rg	37.89 Å
Shape Rg shape_rg	37.84 Å
Total Rg total_rg	38.26 Å
Total atoms total_atoms	16163
Residues n_residues	1998
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	124.1 Å
Rg (real space) rg_real	38.35 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	8.1100e+08
I(0) uncertainty (real space) i0_real_error	1.3880e+07
Rg (reciprocal space) rg_reciprocal	38.42 Å
I(0) (reciprocal space) i0_reciprocal	811100000.0000
Solution quality estimate total_estimate	0.8968
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.541
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	266600000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.948

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	Nitrogenase protein alpha chain
Molecular weight formula_weight	56467.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	18458

MTHHHHHHHHGMSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFRQMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWEASEGAEKVAASA

来源 Source

来源生物 organism	Azotobacter vinelandii DJ
NCBI Class编号 ncbi_taxonomy_id	322710
宿主生物 host_organism	Azotobacter vinelandii DJ

Entity 2 Entity 2 polymer

Description description	Nitrogenase molybdenum-iron protein beta chain
Molecular weight formula_weight	59419.8 kDa
EC 编号 ec_number	1.18.6.1
Mutation mutation	D353G and D357G
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MSQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVGMMTGSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR

来源 Source

来源生物 organism	Azotobacter vinelandii DJ
NCBI Class编号 ncbi_taxonomy_id	322710
宿主生物 host_organism	Azotobacter vinelandii DJ

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	35

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	3-HYDROXY-3-CARBOXY-ADIPIC ACID
Molecular weight formula_weight	206.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	iron-sulfur-molybdenum cluster with interstitial carbon
Molecular weight formula_weight	787.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	FE(8)-S(7) CLUSTER, OXIDIZED
Molecular weight formula_weight	671.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	FE(8)-S(7) CLUSTER
Molecular weight formula_weight	671.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2173

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8. Citations (1)

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Unit-cell length a length_a	167.486 Å
Unit-cell length b length_b	74.469 Å
Unit-cell length c length_c	208.467 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	48.320 Å
R factor r_factor	0.1566
R_work r_work	0.1550
R_free r_free	0.1872

fit	/app/data/saxs_computation/p8/8p8g/8p8g.fit
pddf	/app/data/pr_computation/p8/8p8g/8p8g.pr.out
profile	/app/data/saxs_computation/p8/8p8g/8p8g.dat

Nitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G

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

Nitrogenase protein alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Nitrogenase molybdenum-iron protein beta chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)