2ybv

STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS

Method: X-RAY DIFFRACTION D_max: 134.3 Å Quality: GOOD

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

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

THERMOSYNECHOCOCCUS ELONGATUS

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 × 16 PDB 声明：hexadecameric（16）与蛋白拷贝数一致	链 A； UniProt 1–475 链 C； UniProt 1–475 链 E； UniProt 1–475 链 G； UniProt 1–475 链 I； UniProt 1–475 链 K； UniProt 1–475 链 M； UniProt 1–475 链 O； UniProt 1–475	未记录	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT × 8 （Q8DIS7） CL CHLORIDE ION × 15	X-RAY DIFFRACTION X-ray结晶条件：pH 7；5% PEG8000, 20% PEG200, 10% GLYCEROL, 100MM HEPES, PH 7	分辨率 2.30 Å R-free 0.232

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 2YBV	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
3ZXW STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE 提交 2011-08-16	构建体不同突变/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 × 16 PDB 声明：hexadecameric	链 A 1–475（475 aa）链 C 1–475（475 aa）链 E 1–475（475 aa）链 G 1–475（475 aa）	非标准单体：是（mmCIF未提供具体位点）非标准单体：是（mmCIF未提供具体位点）非标准单体：是（mmCIF未提供具体位点）非标准单体：是（mmCIF未提供具体位点）	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 GOL GLYCEROL × 22	X-RAY DIFFRACTION X-ray结晶条件 pH 8；80 MM HEPES, 20 MM MGCL2, 8% (W/V) PEG4000, 30% (V/V) GLYCEROL, PH=8	分辨率 2.10 Å R-free 0.213
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/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 × 16 PDB 声明：hexadecameric	链 A1 1–475（475 aa）片段：RbcL 链 A2 1–475（475 aa）片段：RbcL 链 A3 1–475（475 aa）片段：RbcL 链 A4 1–475（475 aa）片段：RbcL 链 A5 1–475（475 aa）片段：RbcL 链 A6 1–475（475 aa）片段：RbcL 链 A7 1–475（475 aa）片段：RbcL 链 A8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 10 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 S1 1–475（475 aa）片段：RbcL 链 S2 1–475（475 aa）片段：RbcL 链 S3 1–475（475 aa）片段：RbcL 链 S4 1–475（475 aa）片段：RbcL 链 S5 1–475（475 aa）片段：RbcL 链 S6 1–475（475 aa）片段：RbcL 链 S7 1–475（475 aa）片段：RbcL 链 S8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 C1 1–475（475 aa）片段：RbcL 链 C2 1–475（475 aa）片段：RbcL 链 C3 1–475（475 aa）片段：RbcL 链 C4 1–475（475 aa）片段：RbcL 链 C5 1–475（475 aa）片段：RbcL 链 C6 1–475（475 aa）片段：RbcL 链 C7 1–475（475 aa）片段：RbcL 链 C8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 E1 1–475（475 aa）片段：RbcL 链 E2 1–475（475 aa）片段：RbcL 链 E3 1–475（475 aa）片段：RbcL 链 E4 1–475（475 aa）片段：RbcL 链 E5 1–475（475 aa）片段：RbcL 链 E6 1–475（475 aa）片段：RbcL 链 E7 1–475（475 aa）片段：RbcL 链 E8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 G1 1–475（475 aa）片段：RbcL 链 G2 1–475（475 aa）片段：RbcL 链 G3 1–475（475 aa）片段：RbcL 链 G4 1–475（475 aa）片段：RbcL 链 G5 1–475（475 aa）片段：RbcL 链 G6 1–475（475 aa）片段：RbcL 链 G7 1–475（475 aa）片段：RbcL 链 G8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 I1 1–475（475 aa）片段：RbcL 链 I2 1–475（475 aa）片段：RbcL 链 I3 1–475（475 aa）片段：RbcL 链 I4 1–475（475 aa）片段：RbcL 链 I5 1–475（475 aa）片段：RbcL 链 I6 1–475（475 aa）片段：RbcL 链 I7 1–475（475 aa）片段：RbcL 链 I8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 6 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 K1 1–475（475 aa）片段：RbcL 链 K2 1–475（475 aa）片段：RbcL 链 K3 1–475（475 aa）片段：RbcL 链 K4 1–475（475 aa）片段：RbcL 链 K5 1–475（475 aa）片段：RbcL 链 K6 1–475（475 aa）片段：RbcL 链 K7 1–475（475 aa）片段：RbcL 链 K8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 7 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 M1 1–475（475 aa）片段：RbcL 链 M2 1–475（475 aa）片段：RbcL 链 M3 1–475（475 aa）片段：RbcL 链 M4 1–475（475 aa）片段：RbcL 链 M5 1–475（475 aa）片段：RbcL 链 M6 1–475（475 aa）片段：RbcL 链 M7 1–475（475 aa）片段：RbcL 链 M8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 8 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 O1 1–475（475 aa）片段：RbcL 链 O2 1–475（475 aa）片段：RbcL 链 O3 1–475（475 aa）片段：RbcL 链 O4 1–475（475 aa）片段：RbcL 链 O5 1–475（475 aa）片段：RbcL 链 O6 1–475（475 aa）片段：RbcL 链 O7 1–475（475 aa）片段：RbcL 链 O8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus 提交 2017-09-26	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 9 蛋白异源复合物异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 Q1 1–475（475 aa）片段：RbcL 链 Q2 1–475（475 aa）片段：RbcL 链 Q3 1–475（475 aa）片段：RbcL 链 Q4 1–475（475 aa）片段：RbcL 链 Q5 1–475（475 aa）片段：RbcL 链 Q6 1–475（475 aa）片段：RbcL 链 Q7 1–475（475 aa）片段：RbcL 链 Q8 1–475（475 aa）片段：RbcL	突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A 突变：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	分辨率 2.63 Å R-free 0.274

共 2 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	RBL_THEEB
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–475； UniProt 1–475 作者链 C； PDB构建体 1–475； UniProt 1–475 作者链 E； PDB构建体 1–475； UniProt 1–475 作者链 G； PDB构建体 1–475； UniProt 1–475 作者链 I； PDB构建体 1–475； UniProt 1–475 作者链 K； PDB构建体 1–475； UniProt 1–475 作者链 M； PDB构建体 1–475； UniProt 1–475 作者链 O； PDB构建体 1–475； UniProt 1–475

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT

THERMOSYNECHOCOCCUS ELONGATUS

UniProt Q8DIS7

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 × 16 PDB 声明：hexadecameric（16）与蛋白拷贝数一致	链 B； UniProt 1–118 链 D； UniProt 1–118 链 F； UniProt 1–118 链 H； UniProt 1–118 链 J； UniProt 1–118 链 L； UniProt 1–118 链 N； UniProt 1–118 链 P； UniProt 1–118	未记录	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN × 8 （Q8DIS5） CL CHLORIDE ION × 15	X-RAY DIFFRACTION X-ray结晶条件：pH 7；5% PEG8000, 20% PEG200, 10% GLYCEROL, 100MM HEPES, PH 7	分辨率 2.30 Å R-free 0.232

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 2YBV	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
3ZXW STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE 提交 2011-08-16	构建体不同突变/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 × 16 PDB 声明：hexadecameric	链 B 1–118（118 aa）链 D 1–118（118 aa）链 F 1–118（118 aa）链 H 1–118（118 aa）	未记录	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 GOL GLYCEROL × 22	X-RAY DIFFRACTION X-ray结晶条件 pH 8；80 MM HEPES, 20 MM MGCL2, 8% (W/V) PEG4000, 30% (V/V) GLYCEROL, PH=8	分辨率 2.10 Å R-free 0.213

共 1 个其他 PDB 条目、1 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	Q8DIS7_THEEB
Isoform	—
PDB实体	2
链与序列区间	作者链 B； PDB构建体 1–118； UniProt 1–118 作者链 D； PDB构建体 1–118； UniProt 1–118 作者链 F； PDB构建体 1–118； UniProt 1–118 作者链 H； PDB构建体 1–118； UniProt 1–118 作者链 J； PDB构建体 1–118； UniProt 1–118 作者链 L； PDB构建体 1–118； UniProt 1–118 作者链 N； PDB构建体 1–118； UniProt 1–118 作者链 P； PDB构建体 1–118； UniProt 1–118

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	2ybv
沉积日期 deposition_date	2011-03-10
结构标题 title	STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS
关键词 keywords	;CO2/O2 SPECIFICITY, CARBON DIOXIDE FIXATION, PHOTOSYNTHESIS, THERMOSTABILITY, PHOTORESPIRATION, MONOOXYGENASE, HYDROXYLATION, OXIDOREDUCTASE, LYASE, RUBISCO, CHLOROPLAST, CALVIN CYCLE, THERMOPHILIC CYANOBACTERIA ;; LYASE
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	47.10 Å
回转半径 Rg (电子) rg_electron	46.18 Å
零角强度 I(0) i0	3313680000.00
分子量 molecular_weight	479880.0 kDa
排除体积 excluded_volume	598630 Å³
包络体积 envelope_volume	747730 Å³
水化壳体积 shell_volume	122720 Å³
包络直径 envelope_diameter	137.3 Å
壳层 Rg shell_rg	58.90 Å
包络 Rg envelope_rg	45.63 Å
形状 Rg shape_rg	46.20 Å
总 Rg total_rg	46.47 Å
总原子数 total_atoms	33751
残基数 n_residues	4256
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	134.3 Å
Rg (实空间) rg_real	46.62 Å
Rg 误差 (实空间) rg_real_error	0.37 Å
I(0) (实空间) i0_real	3.3140e+09
I(0) 误差 (实空间) i0_real_error	4.4660e+07
Rg (倒空间) rg_reciprocal	47.09 Å
I(0) (倒空间) i0_reciprocal	3316000000.0000
解质量估计 total_estimate	0.8655
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	65.1 Å
偏度 Skewness skewness	-0.021
峰度 Kurtosis kurtosis	-0.557
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	1117000000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.433

▶

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

▶

6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
分子量 formula_weight	53091.3 kDa
EC 编号 ec_number	4.1.1.39
来源方法 src_method	man
拷贝数 entity_count	8

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K,M,O
原子数 atom_count	34583

MAYTQSKSQKVGYQAGVKDYRLTYYTPDYTPKDTDILAAFRVTPQPGVPFEEAAAAVAAESSTGTWTTVWTDLLTDLDRYKGCCYDIEPLPGEDNQFIAYIAYPLDLFEEGSVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKELEMPIIMHDFLTAGFTANTTLSKWCRDNGMLLHIHRAMHAVMDRQKNHGIHFRVLAKCLRMSGGDHIHTGTVVGKLEGDKAVTLGFVDLLRENYIEQDRSRGIYFTQDWASMPGVMAVASGGIHVWHMPALVDIFGDDAVLQFGGGTLGHPWGNAPGATANRVALEACIQARNEGRDLMREGGDIIREAARWSPELAAACELWKEIKFEFEAQDTI

来源 Source

来源生物 organism	THERMOSYNECHOCOCCUS ELONGATUS
NCBI 分类编号 ncbi_taxonomy_id	197221
宿主生物 host_organism	ESCHERICHIA COLI

实体 2 Entity 2 polymer

描述 description	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
分子量 formula_weight	13999.8 kDa
EC 编号 ec_number	4.1.1.39
来源方法 src_method	man
拷贝数 entity_count	8

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,J,L,N,P

MKTLPKERRYETFSYLPPLSDAQIARQIQYAIDQGYHPCVEFNETSNAEIRYWTMWKLPLFNCTNAQDVLNEVQQCRSEYPNCFIRVVAFDNIKQCQVMSFIVYKPNQANSGYSGYRY

来源 Source

来源生物 organism	THERMOSYNECHOCOCCUS ELONGATUS
NCBI 分类编号 ncbi_taxonomy_id	197221
宿主生物 host_organism	ESCHERICHIA COLI

实体 3 Entity 3 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	15

实体 4 Entity 4 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	832

▼

7. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

结构域编号 domain_id	d2ybva1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
家族 Family family	d.58.9.0 — automated matches

结构域编号 domain_id	d2ybva2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
家族 Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

结构域编号 domain_id	d2ybvb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.73 — RuBisCO, small subunit
超家族 Superfamily superfamily	d.73.1 — RuBisCO, small subunit
家族 Family family	d.73.1.1 — RuBisCO, small subunit

结构域编号 domain_id	d2ybvc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
家族 Family family	d.58.9.0 — automated matches

结构域编号 domain_id	d2ybvc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
家族 Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

结构域编号 domain_id	d2ybvd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.73 — RuBisCO, small subunit
超家族 Superfamily superfamily	d.73.1 — RuBisCO, small subunit
家族 Family family	d.73.1.1 — RuBisCO, small subunit

结构域编号 domain_id	d2ybve1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
家族 Family family	d.58.9.0 — automated matches

结构域编号 domain_id	d2ybve2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
家族 Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

结构域编号 domain_id	d2ybvf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.73 — RuBisCO, small subunit
超家族 Superfamily superfamily	d.73.1 — RuBisCO, small subunit
家族 Family family	d.73.1.1 — RuBisCO, small subunit

结构域编号 domain_id	d2ybvg1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
家族 Family family	d.58.9.0 — automated matches

结构域编号 domain_id	d2ybvg2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
家族 Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

结构域编号 domain_id	d2ybvh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.73 — RuBisCO, small subunit
超家族 Superfamily superfamily	d.73.1 — RuBisCO, small subunit
家族 Family family	d.73.1.1 — RuBisCO, small subunit

结构域编号 domain_id	d2ybvi1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
家族 Family family	d.58.9.0 — automated matches

结构域编号 domain_id	d2ybvi2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
家族 Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

结构域编号 domain_id	d2ybvj_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.73 — RuBisCO, small subunit
超家族 Superfamily superfamily	d.73.1 — RuBisCO, small subunit
家族 Family family	d.73.1.1 — RuBisCO, small subunit

结构域编号 domain_id	d2ybvk1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
家族 Family family	d.58.9.0 — automated matches

结构域编号 domain_id	d2ybvk2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
家族 Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

结构域编号 domain_id	d2ybvl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.73 — RuBisCO, small subunit
超家族 Superfamily superfamily	d.73.1 — RuBisCO, small subunit
家族 Family family	d.73.1.1 — RuBisCO, small subunit

结构域编号 domain_id	d2ybvm1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
家族 Family family	d.58.9.0 — automated matches

结构域编号 domain_id	d2ybvm2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
家族 Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

结构域编号 domain_id	d2ybvn_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.73 — RuBisCO, small subunit
超家族 Superfamily superfamily	d.73.1 — RuBisCO, small subunit
家族 Family family	d.73.1.1 — RuBisCO, small subunit

结构域编号 domain_id	d2ybvo1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
家族 Family family	d.58.9.0 — automated matches

结构域编号 domain_id	d2ybvo2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
家族 Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

结构域编号 domain_id	d2ybvp_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.73 — RuBisCO, small subunit
超家族 Superfamily superfamily	d.73.1 — RuBisCO, small subunit
家族 Family family	d.73.1.1 — RuBisCO, small subunit

CATH v4.4 (24 domains)

结构域编号 domain_id	2ybvA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

结构域编号 domain_id	2ybvA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

结构域编号 domain_id	2ybvB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
同源超家族 H-superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

结构域编号 domain_id	2ybvC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

结构域编号 domain_id	2ybvC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

结构域编号 domain_id	2ybvD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
同源超家族 H-superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

结构域编号 domain_id	2ybvE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

结构域编号 domain_id	2ybvE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

结构域编号 domain_id	2ybvF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
同源超家族 H-superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

结构域编号 domain_id	2ybvG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

结构域编号 domain_id	2ybvG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

结构域编号 domain_id	2ybvH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
同源超家族 H-superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

结构域编号 domain_id	2ybvI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

结构域编号 domain_id	2ybvI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

结构域编号 domain_id	2ybvJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
同源超家族 H-superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

结构域编号 domain_id	2ybvK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

结构域编号 domain_id	2ybvK02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

结构域编号 domain_id	2ybvL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
同源超家族 H-superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

结构域编号 domain_id	2ybvM01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

结构域编号 domain_id	2ybvM02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

结构域编号 domain_id	2ybvN00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
同源超家族 H-superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

结构域编号 domain_id	2ybvO01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

结构域编号 domain_id	2ybvO02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

结构域编号 domain_id	2ybvP00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
同源超家族 H-superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	115.480 Å
晶胞边长 b length_b	163.470 Å
晶胞边长 c length_c	163.540 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	108.96 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	39.840 Å
R 因子 r_factor	0.1976
R_work r_work	0.1958
R_free r_free	0.2317

STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS

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

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

当前结构中的状态

数据库中的同蛋白其他状态

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL 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 (4)

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 water

7. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/yb/2ybv/2ybv.fit
pddf	/app/data/pr_computation/yb/2ybv/2ybv.pr.out
profile	/app/data/saxs_computation/yb/2ybv/2ybv.dat