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. 蛋白身份与相关结构 Protein Identity & Related Structures

Nitrogenase protein alpha chain

Azotobacter vinelandii DJ

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白异源复合物异源复合物蛋白 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链 A； UniProt 3–492 链 C； UniProt 3–492	未记录	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结晶条件：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.	分辨率 1.55 Å R-free 0.187

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 8P8G	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
8BTS Nitrogenase MoFe protein from A. vinelandii alpha double mutant C45A/L158C 提交 2022-11-29	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 3–492（490 aa）链 C 3–492（490 aa）	未记录	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结晶条件 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.	分辨率 3.03 Å R-free 0.223
8BTS Nitrogenase MoFe protein from A. vinelandii alpha double mutant C45A/L158C 提交 2022-11-29	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 H 3–492（490 aa）链 J 3–492（490 aa）	未记录	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结晶条件 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.	分辨率 3.03 Å R-free 0.223

共 1 个其他 PDB 条目、2 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	C1DGZ7_AZOVD
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 11–500； UniProt 3–492 作者链 C； PDB构建体 11–500； UniProt 3–492

Nitrogenase molybdenum-iron protein beta chain

Azotobacter vinelandii DJ

UniProt C1DGZ8

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白异源复合物异源复合物蛋白 × 4 PDB 声明：tetrameric（4）与蛋白拷贝数一致	链 B； UniProt 1–523 链 D； UniProt 1–523	突变：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结晶条件：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.	分辨率 1.55 Å R-free 0.187

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 8P8G	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
7MCI MoFe protein from Azotobacter vinelandii with a sulfur-replenished cofactor 提交 2021-04-02	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	未记录	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结晶条件 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	分辨率 1.65 Å R-free 0.195
7UT6 C1 symmetric cryoEM structure of Azotobacter vinelandii MoFeP under non-turnover conditions 提交 2022-04-26	突变/修饰不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	未记录	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缓冲液 pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	分辨率 1.91 Å
7UT7 C2 symmetric cryoEM structure of Azotobacter vinelandii MoFeP under non-turnover conditions 提交 2022-04-26	突变/修饰不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	未记录	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缓冲液 pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	分辨率 1.91 Å
7UT8 CryoEM structure of Azotobacter vinelandii nitrogenase complex (1:1 FeP:MoFeP, ATP-bound) during catalytic N2 reduction 提交 2022-04-26	突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 6 PDB 声明：hexameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	未记录	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缓冲液 pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	分辨率 2.43 Å
7UT9 CryoEM structure of Azotobacter vinelandii nitrogenase complex (1:1 FeP:MoFeP, ADP/ATP-bound) during catalytic N2 reduction 提交 2022-04-26	突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 6 PDB 声明：hexameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	未记录	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缓冲液 pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	分辨率 2.44 Å
7UTA CryoEM structure of Azotobacter vinelandii nitrogenase complex (2:1 FeP:MoFeP) inhibited by BeFx during catalytic N2 reduction 提交 2022-04-26	突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 8 PDB 声明：octameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	未记录	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缓冲液 pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	分辨率 2.40 Å
8DPN CryoEM structure of Azotobacter vinelandii nitrogenase MoFeP during catalytic N2 reduction 提交 2022-07-15	突变/修饰不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	未记录	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缓冲液 pH 8；Solutions were prepared and filtered immediately prior to the experiment. cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE；Custom manual plunger. Greater than 95% humidity.	分辨率 2.49 Å
8E3T Gallium-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation 提交 2022-08-17	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	突变：S188A 突变：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结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% PEG 8000, 100 mM Tris pH 8.5, 500 mM NaCl, 10 mM dithionite	分辨率 2.20 Å R-free 0.243
8E3U Nickel-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation 提交 2022-08-17	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	突变：S188A 突变：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结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.25；293 K；18% PEG 8000, 100 mM Tris pH 8.25, 500 mM NaCl, 10 mM dithionite	分辨率 1.99 Å R-free 0.253
8E3V Cobalt-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation 提交 2022-08-17	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 1–523（523 aa）链 D 1–523（523 aa）	突变：S188A 突变：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结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.75；293 K；20% PEG 8000, 100 mM Tris pH 7.75, 500 mM NaCl, 10 mM dithionite	分辨率 2.00 Å R-free 0.208
8ENN Homocitrate-deficient nitrogenase MoFe-protein from Azotobacter vinelandii nifV knockout 提交 2022-09-30	构建体不同突变/修饰不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 B 2–523（522 aa）链 D 2–523（522 aa）	未记录	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缓冲液 pH 7.8 cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE	分辨率 2.58 Å
8ENO Homocitrate-deficient nitrogenase MoFe-protein from A. vinelandii nifV knockout in complex with NafT 提交 2022-09-30	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 B 2–523（522 aa）链 D 2–523（522 aa）	未记录	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缓冲液 pH 7.8 cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE	分辨率 2.71 Å

共 12 个其他 PDB 条目、12 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	C1DGZ8_AZOVD
Isoform	—
PDB实体	2
链与序列区间	作者链 B； PDB构建体 1–523； UniProt 1–523 作者链 D； PDB构建体 1–523； UniProt 1–523

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	8p8g
沉积日期 deposition_date	2023-06-01
最后修订 last_revision	2023-12-13
结构标题 title	Nitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G
关键词 keywords	Molybdenum nitrogenase, N2-fixation, FeMocofactor, metal binding site, P cluster, NH3 production, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	38.46 Å
回转半径 Rg (电子) rg_electron	37.84 Å
零角强度 I(0) i0	811038000.00
分子量 molecular_weight	232020.0 kDa
排除体积 excluded_volume	288920 Å³
包络体积 envelope_volume	333750 Å³
水化壳体积 shell_volume	70028 Å³
包络直径 envelope_diameter	125.6 Å
壳层 Rg shell_rg	46.28 Å
包络 Rg envelope_rg	37.89 Å
形状 Rg shape_rg	37.84 Å
总 Rg total_rg	38.26 Å
总原子数 total_atoms	16163
残基数 n_residues	1998
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	124.1 Å
Rg (实空间) rg_real	38.35 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	8.1100e+08
I(0) 误差 (实空间) i0_real_error	1.3880e+07
Rg (倒空间) rg_reciprocal	38.42 Å
I(0) (倒空间) i0_reciprocal	811100000.0000
解质量估计 total_estimate	0.8968
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.253
峰度 Kurtosis kurtosis	-0.541
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	266600000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 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. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (12)

实体 1 Entity 1 polymer

描述 description	Nitrogenase protein alpha chain
分子量 formula_weight	56467.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	18458

MTHHHHHHHHGMSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFRQMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWEASEGAEKVAASA

来源 Source

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

实体 2 Entity 2 polymer

描述 description	Nitrogenase molybdenum-iron protein beta chain
分子量 formula_weight	59419.8 kDa
EC 编号 ec_number	1.18.6.1
突变 mutation	D353G and D357G
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	B,D

MSQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVGMMTGSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR

来源 Source

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

实体 3 Entity 3 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	35

实体 4 Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 5 Entity 5 non-polymer

描述 description	3-HYDROXY-3-CARBOXY-ADIPIC ACID
分子量 formula_weight	206.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 6 Entity 6 non-polymer

描述 description	iron-sulfur-molybdenum cluster with interstitial carbon
分子量 formula_weight	787.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 7 Entity 7 non-polymer

描述 description	1,4-DIETHYLENE DIOXIDE
分子量 formula_weight	88.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 8 Entity 8 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 9 Entity 9 non-polymer

描述 description	FE(8)-S(7) CLUSTER, OXIDIZED
分子量 formula_weight	671.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 10 Entity 10 non-polymer

描述 description	FE(8)-S(7) CLUSTER
分子量 formula_weight	671.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 11 Entity 11 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 12 Entity 12 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2173

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	167.486 Å
晶胞边长 b length_b	74.469 Å
晶胞边长 c length_c	208.467 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.25 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.550 Å
最低分辨率 resolution_low	48.320 Å
R 因子 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. 蛋白身份与相关结构 Protein Identity & Related Structures

Nitrogenase protein alpha chain

当前结构中的状态

数据库中的同蛋白其他状态

Nitrogenase molybdenum-iron protein beta chain

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (12)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 polymer

聚合物 Polymer

来源 Source

实体 3 Entity 3 non-polymer

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 non-polymer

实体 8 Entity 8 non-polymer

实体 9 Entity 9 non-polymer

实体 10 Entity 10 non-polymer

实体 11 Entity 11 non-polymer

实体 12 Entity 12 water

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)