4ko4

High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

Method: X-RAY DIFFRACTION D_max: 120.5 Å Quality: GOOD

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

Periplasmic [NiFeSe] hydrogenase small subunit

物种未注明

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 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 S； UniProt 33–315	未记录	Nickel-dependent hydrogenase large subunit × 1 （C7LN88） SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 2.00 Å R-free 0.172
2	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 T； UniProt 33–315	未记录	Nickel-dependent hydrogenase large subunit × 1 （C7LN88） SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 2.00 Å R-free 0.172

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 4KO4	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
1CC1 CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM 提交 1999-03-03	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 × 2 PDB 声明：dimeric	链 S 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 NI NICKEL (II) ION × 1 FE2 FE (II) ION × 1 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 6.2；pH 6.2	分辨率 2.15 Å R-free 0.248
4KL8 High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-07	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 × 2 PDB 声明：dimeric	链 S 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.52 Å R-free 0.171
4KL8 High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-07	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 × 2 PDB 声明：dimeric	链 T 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.52 Å R-free 0.171
4KN9 High-resolution structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-09	结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 S 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.40 Å R-free 0.168
4KN9 High-resolution structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-09	配体/离子不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 T 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.40 Å R-free 0.168
4KO1 High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	配体/离子不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 S 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.55 Å R-free 0.184
4KO1 High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	配体/离子不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 T 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.55 Å R-free 0.184
4KO2 Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	配体/离子不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 S 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.60 Å R-free 0.194
4KO2 Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	配体/离子不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 T 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.60 Å R-free 0.194
4KO3 Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 S 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.70 Å R-free 0.201
4KO3 Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 T 33–315（283 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.70 Å R-free 0.201

共 6 个其他 PDB 条目、11 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	PHSS_DESBA
Isoform	—
PDB实体	1
链与序列区间	作者链 S； PDB构建体 1–283； UniProt 33–315 作者链 T； PDB构建体 1–283； UniProt 33–315

Nickel-dependent hydrogenase large subunit

物种未注明

UniProt C7LN88

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 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 L； UniProt 1–499	未记录	Periplasmic [NiFeSe] hydrogenase small subunit × 1 （P13063） SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 2.00 Å R-free 0.172
2	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 M； UniProt 1–499	未记录	Periplasmic [NiFeSe] hydrogenase small subunit × 1 （P13063） SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 2.00 Å R-free 0.172

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 4KO4	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
4KL8 High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-07	突变/修饰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 × 2 PDB 声明：dimeric	链 L 1–499（499 aa）	非标准单体：是（mmCIF未提供具体位点）	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.52 Å R-free 0.171
4KL8 High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-07	突变/修饰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 × 2 PDB 声明：dimeric	链 M 1–499（499 aa）	非标准单体：是（mmCIF未提供具体位点）	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.52 Å R-free 0.171
4KN9 High-resolution structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-09	结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 L 1–499（499 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.40 Å R-free 0.168
4KN9 High-resolution structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-09	配体/离子不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 M 1–499（499 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.40 Å R-free 0.168
4KO1 High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	配体/离子不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 L 1–499（499 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.55 Å R-free 0.184
4KO1 High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	配体/离子不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 M 1–499（499 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.55 Å R-free 0.184
4KO2 Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	配体/离子不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 L 1–499（499 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.60 Å R-free 0.194
4KO2 Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	配体/离子不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 M 1–499（499 aa）	未记录	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 4 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.60 Å R-free 0.194
4KO3 Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	突变/修饰不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 L 1–499（499 aa）	非标准单体：是（mmCIF未提供具体位点）	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.70 Å R-free 0.201
4KO3 Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air 提交 2013-05-11	突变/修饰不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 M 1–499（499 aa）	非标准单体：是（mmCIF未提供具体位点）	SF4 IRON/SULFUR CLUSTER × 3 CA CALCIUM ION × 5 GOL GLYCEROL × 2 FCO CARBONMONOXIDE-(DICYANO) IRON × 1 NI NICKEL (II) ION × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	分辨率 1.70 Å R-free 0.201

共 5 个其他 PDB 条目、10 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	C7LN88_DESBD
Isoform	—
PDB实体	2
链与序列区间	作者链 L； PDB构建体 1–499； UniProt 1–499 作者链 M； PDB构建体 1–499； UniProt 1–499

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	4ko4
沉积日期 deposition_date	2013-05-11
结构标题 title	High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air
关键词 keywords	NIFESE-SITE, H2 CLEAVAGE/PRODUCTION, SELENINATE, 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	37.09 Å
回转半径 Rg (电子) rg_electron	36.59 Å
零角强度 I(0) i0	450765000.00
分子量 molecular_weight	171890.0 kDa
排除体积 excluded_volume	214110 Å³
包络体积 envelope_volume	252750 Å³
水化壳体积 shell_volume	56360 Å³
包络直径 envelope_diameter	126.2 Å
壳层 Rg shell_rg	43.71 Å
包络 Rg envelope_rg	36.47 Å
形状 Rg shape_rg	36.58 Å
总 Rg total_rg	37.02 Å
总原子数 total_atoms	11985
残基数 n_residues	1534
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	120.5 Å
Rg (实空间) rg_real	37.13 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	4.5080e+08
I(0) 误差 (实空间) i0_real_error	7.0780e+06
Rg (倒空间) rg_reciprocal	37.11 Å
I(0) (倒空间) i0_reciprocal	450800000.0000
解质量估计 total_estimate	0.8826
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	36.4 Å
偏度 Skewness skewness	0.342
峰度 Kurtosis kurtosis	-0.560
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	149900000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.862

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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 (10)

实体 1 Entity 1 polymer

描述 description	Periplasmic [NiFeSe] hydrogenase small subunit
分子量 formula_weight	30874.1 kDa
EC 编号 ec_number	1.12.99.6
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	S,T
原子数 atom_count	14237

MTEGAKKAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKGHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHVLNPTEHPLPELDDDGRPLLFFGDNIHENCPYLDKYDNSEFAETFTKPGCKAELGCKGPSTYADCAKRRWNNGINWCVENAVCIGCVEPDFPDGKSPFYVAE

实体 2 Entity 2 polymer

描述 description	Nickel-dependent hydrogenase large subunit
分子量 formula_weight	55291.8 kDa
EC 编号 ec_number	1.18.99.1
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

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

MSQAATPAADGKVKISIDPLTRVEGHLKIEVEVKDGKVVDAKCSGGMFRGFEQILRGRDPRDSSQIVQRICGVCPTAHCTASVMAQDDAFGVKVTTNGRITRNLIFGANYLQSHILHFYHLAALDYVKGPDVSPFVPRYANADLLTDRIKDGAKADATNTYGLNQYLKALEIRRICHEMVAMFGGRMPHVQGMVVGGATEIPTADKVAEYAARFKEVQKFVIEEYLPLIYTLGSVYTDLFETGIGWKNVIAFGVFPEDDDYKTFLLKPGVYIDGKDEEFDSKLVKEYVGHSFFDHSAPGGLHYSVGETNPNPDKPGAYSFVKAPRYKDKPCEVGPLARMWVQNPELSPVGQKLLKELYGIEAKNFRDLGDKAFSIMGRHVARAEETWLTAVAVEKWLKQVQPGAETYVKSEIPDAAEGTGFTEAPRGALLHYLKIKDKKIENYQIVSATLWNANPRDDMGQRGPIEEALIGVPVPDIKNPVNVGRLVRSYDPULGCAVH

实体 3 Entity 3 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

实体 4 Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

实体 5 Entity 5 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	1

实体 6 Entity 6 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	4

实体 7 Entity 7 non-polymer

描述 description	CARBONMONOXIDE-(DICYANO) IRON
分子量 formula_weight	135.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 8 Entity 8 non-polymer

描述 description	NICKEL (II) ION
分子量 formula_weight	58.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 9 Entity 9 non-polymer

描述 description	HYDROSULFURIC ACID
分子量 formula_weight	34.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 10 Entity 10 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	1844

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7. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d4ko4l_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.18 — HydB/Nqo4-like
超家族 Superfamily superfamily	e.18.1 — HydB/Nqo4-like
家族 Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

结构域编号 domain_id	d4ko4m_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.18 — HydB/Nqo4-like
超家族 Superfamily superfamily	e.18.1 — HydB/Nqo4-like
家族 Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

结构域编号 domain_id	d4ko4s_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.19 — HydA/Nqo6-like
超家族 Superfamily superfamily	e.19.1 — HydA/Nqo6-like
家族 Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

结构域编号 domain_id	d4ko4t_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.19 — HydA/Nqo6-like
超家族 Superfamily superfamily	e.19.1 — HydA/Nqo6-like
家族 Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

CATH v4.4 (6 domains)

结构域编号 domain_id	4ko4L00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

结构域编号 domain_id	4ko4M00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

结构域编号 domain_id	4ko4S01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

结构域编号 domain_id	4ko4S02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

结构域编号 domain_id	4ko4T01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

结构域编号 domain_id	4ko4T02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

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8. 引用文献 (2)

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晶胞边长 a length_a	106.200 Å
晶胞边长 b length_b	108.720 Å
晶胞边长 c length_c	136.620 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.1495
R_work r_work	0.1484
R_free r_free	0.1719

fit	/app/data/saxs_computation/ko/4ko4/4ko4.fit
pddf	/app/data/pr_computation/ko/4ko4/4ko4.pr.out
profile	/app/data/saxs_computation/ko/4ko4/4ko4.dat

High X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

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

Periplasmic [NiFeSe] hydrogenase small subunit

当前结构中的状态

数据库中的同蛋白其他状态

Nickel-dependent hydrogenase large subunit

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 (10)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

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 water

7. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. 引用文献 (2)

9. 文件与曲线 (10)

Files (7)

Curves (3)