1upm

ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.

Method: X-RAY DIFFRACTION D_max: 140.0 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

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 × 16 PDB 声明：hexadecameric（16）与蛋白拷贝数一致	链 B； UniProt 1–475 链 E； UniProt 1–475 链 H； UniProt 1–475 链 K； UniProt 1–475 链 L； UniProt 1–475 链 O； UniProt 1–475 链 R； UniProt 1–475 链 V； UniProt 1–475	非标准单体：是（mmCIF未提供具体位点）	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN × 8 （Q43832） CA CALCIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件：pH 7.8；10% PEG 4000, 0.1 M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 1MM 2-CABP	分辨率 2.30 Å R-free 0.200

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 1UPM	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
1AA1 ACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGLYCERATE 提交 1997-01-20	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 1–475（475 aa）链 E 1–475（475 aa）链 H 1–475（475 aa）链 L 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 3PG 3-PHOSPHOGLYCERIC ACID × 16	X-RAY DIFFRACTION X-ray结晶条件 pH 7.2；14% PEG 4000, 0.2 M NACL, 25 MM HEPES PH 7.8 10 MM MGCL2, 100 MM 3-PHOSPHOGLYCERATE, pH 7.2	分辨率 2.20 Å R-free 0.224
1AUS ACTIVATED UNLIGANDED SPINACH RUBISCO 提交 1995-06-21	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 L 1–475（475 aa）链 M 1–475（475 aa）链 N 1–475（475 aa）链 O 1–475（475 aa）	未记录	MG MAGNESIUM ION × 8 FMT FORMIC ACID × 8	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.20 Å R-free 0.239
1IR1 Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate 提交 2001-08-31	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 B 1–475（475 aa）链 C 1–475（475 aa）链 D 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	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 7.9；293 K；PEG4000, MgCl2, NaHCO3, DTT, 2-carboxyarabinitol-1,5-bisphosphate, Bicine, pH 7.9, VAPOR DIFFUSION, temperature 293K	分辨率 1.80 Å R-free 0.179
1RBO SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE 提交 1996-10-31	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 1–475（475 aa）链 E 1–475（475 aa）链 H 1–475（475 aa）链 L 1–475（475 aa）	未记录	CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件 pH 7.4；1.7 M (NH4)2SO4, 50 MM PHOSPHATE, PH 7.4 3 MM MGCL2, 25 MM NAHCO3, 10 MM 4CABP	分辨率 2.30 Å R-free 0.171
1RCO SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE 提交 1996-10-31	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 1–475（475 aa）链 E 1–475（475 aa）链 H 1–475（475 aa）链 K 1–475（475 aa）链 L 1–475（475 aa）链 O 1–475（475 aa）链 R 1–475（475 aa）链 V 1–475（475 aa）	未记录	XDP D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件 pH 7.8；15% PEG 4000, 25 MM HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 20 MM XUBP	分辨率 2.30 Å R-free 0.246
1RCX NON-ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE 提交 1996-12-06	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 1–475（475 aa）链 E 1–475（475 aa）链 H 1–475（475 aa）链 K 1–475（475 aa）链 L 1–475（475 aa）链 O 1–475（475 aa）链 R 1–475（475 aa）链 V 1–475（475 aa）	未记录	RUB RIBULOSE-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件 pH 7.8；12% PEG 4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 20 MM RUBP	分辨率 2.40 Å R-free 0.237
1RXO ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM 提交 1996-12-06	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 1–475（475 aa）链 E 1–475（475 aa）链 H 1–475（475 aa）链 L 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）	RUB RIBULOSE-1,5-DIPHOSPHATE × 8 CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray结晶条件 pH 7.8；14% PEG4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 10 MM CACL2; SOAKED WITH 20 MM RUBP FOR 5 DAYS	分辨率 2.20 Å R-free 0.229
1UPP SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium. 提交 2003-10-09	构建体不同突变/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 × 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）	CA CALCIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件 pH 7.8；10% PEG 4000, 0.1M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 0.1 M 3PGA THEN SOAKED IN 2-CABP	分辨率 2.30 Å R-free 0.307
8QJ0 Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO 提交 2023-09-12	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 L 1–475（475 aa）链 M 1–475（475 aa）链 N 1–475（475 aa）链 O 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 × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；SpRub solution at a concentration of 15 mg/mL (in a buffer of 20 mM HEPES, 5 mM MgCl2, pH 8.0), combined reservoir solution (0.2 M MgCl2x6H2O, 0.1 M Tris pH 7.0, 12% w/v PEG 8000	分辨率 2.30 Å R-free 0.227
8RUC ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISPHOSPHATE 提交 1996-02-22	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	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；pH 7.5	分辨率 1.60 Å
9CQ5 Mn-bound RuBisCO from spinach with CABP inhibitor 提交 2024-07-19	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 B 1–475（475 aa）链 C 1–475（475 aa）链 D 1–475（475 aa）链 E 1–475（475 aa）链 F 1–475（475 aa）链 G 1–475（475 aa）链 H 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）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）	MN MANGANESE (II) ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.3；298 K；PEG 3350, lithium acetate, potassium phosphate	分辨率 2.50 Å R-free 0.242

共 11 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_SPIOL
Isoform	—
PDB实体	1
链与序列区间	作者链 B； 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 H； 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 L； PDB构建体 1–475； UniProt 1–475 作者链 O； PDB构建体 1–475； UniProt 1–475 作者链 R； PDB构建体 1–475； UniProt 1–475 作者链 V； PDB构建体 1–475； UniProt 1–475

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

物种未注明

UniProt Q43832

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 C； UniProt 58–180 链 F； UniProt 58–180 链 I； UniProt 58–180 链 M； UniProt 58–180 链 P； UniProt 58–180 链 S； UniProt 58–180 链 T； UniProt 58–180 链 W； UniProt 58–180	未记录	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN × 8 （P00875） CA CALCIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件：pH 7.8；10% PEG 4000, 0.1 M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 1MM 2-CABP	分辨率 2.30 Å R-free 0.200

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 1UPM	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
1AA1 ACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGLYCERATE 提交 1997-01-20	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 C 58–180（123 aa）链 F 58–180（123 aa）链 I 58–180（123 aa）链 S 58–180（123 aa）	未记录	MG MAGNESIUM ION × 8 3PG 3-PHOSPHOGLYCERIC ACID × 16	X-RAY DIFFRACTION X-ray结晶条件 pH 7.2；14% PEG 4000, 0.2 M NACL, 25 MM HEPES PH 7.8 10 MM MGCL2, 100 MM 3-PHOSPHOGLYCERATE, pH 7.2	分辨率 2.20 Å R-free 0.224
1AUS ACTIVATED UNLIGANDED SPINACH RUBISCO 提交 1995-06-21	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 S 58–180（123 aa）链 T 58–180（123 aa）链 U 58–180（123 aa）链 V 58–180（123 aa）	未记录	MG MAGNESIUM ION × 8 FMT FORMIC ACID × 8	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.20 Å R-free 0.239
1IR1 Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate 提交 2001-08-31	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 S 58–180（123 aa）链 T 58–180（123 aa）链 U 58–180（123 aa）链 V 58–180（123 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	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 7.9；293 K；PEG4000, MgCl2, NaHCO3, DTT, 2-carboxyarabinitol-1,5-bisphosphate, Bicine, pH 7.9, VAPOR DIFFUSION, temperature 293K	分辨率 1.80 Å R-free 0.179
1UPP SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium. 提交 2003-10-09	构建体不同突变/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 × 16 PDB 声明：hexadecameric	链 I 58–180（123 aa）链 J 58–180（123 aa）链 K 58–180（123 aa）链 L 58–180（123 aa）	未记录	CA CALCIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件 pH 7.8；10% PEG 4000, 0.1M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 0.1 M 3PGA THEN SOAKED IN 2-CABP	分辨率 2.30 Å R-free 0.307
1UZD Chlamydomonas,Spinach Chimeric Rubisco 提交 2004-03-11	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 信息不足异源复合物；蛋白 × 16 PDB 声明：hexadecameric	链 C 103–121（19 aa）链 F 103–121（19 aa）链 I 103–121（19 aa）链 J 103–121（19 aa）链 M 103–121（19 aa）链 P 103–121（19 aa）链 T 103–121（19 aa）链 W 103–121（19 aa）	未记录	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 54	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；291 K；50 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN	分辨率 2.40 Å R-free 0.230
8QJ0 Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO 提交 2023-09-12	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 S 58–180（123 aa）链 T 58–180（123 aa）链 U 58–180（123 aa）链 V 58–180（123 aa）	未记录	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；SpRub solution at a concentration of 15 mg/mL (in a buffer of 20 mM HEPES, 5 mM MgCl2, pH 8.0), combined reservoir solution (0.2 M MgCl2x6H2O, 0.1 M Tris pH 7.0, 12% w/v PEG 8000	分辨率 2.30 Å R-free 0.227
9CQ5 Mn-bound RuBisCO from spinach with CABP inhibitor 提交 2024-07-19	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 I 58–180（123 aa）链 J 58–180（123 aa）链 K 58–180（123 aa）链 L 58–180（123 aa）链 M 58–180（123 aa）链 N 58–180（123 aa）链 O 58–180（123 aa）链 P 58–180（123 aa）	未记录	MN MANGANESE (II) ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.3；298 K；PEG 3350, lithium acetate, potassium phosphate	分辨率 2.50 Å R-free 0.242

共 7 个其他 PDB 条目、7 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	RBS2_SPIOL
Isoform	—
PDB实体	2
链与序列区间	作者链 C； PDB构建体 1–123； UniProt 58–180 作者链 F； PDB构建体 1–123； UniProt 58–180 作者链 I； PDB构建体 1–123； UniProt 58–180 作者链 M； PDB构建体 1–123； UniProt 58–180 作者链 P； PDB构建体 1–123； UniProt 58–180 作者链 S； PDB构建体 1–123； UniProt 58–180 作者链 T； PDB构建体 1–123； UniProt 58–180 作者链 W； PDB构建体 1–123； UniProt 58–180

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	1upm
沉积日期 deposition_date	2003-10-08
结构标题 title	ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.
关键词 keywords	LYASE, CARBON-CARBON, OXIDOREDUCTASE, PHOTOSYNTHESIS, CARBON-DIOXIDE FIXATION LYASE (CARBON-CARBON); 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	47.33 Å
回转半径 Rg (电子) rg_electron	46.63 Å
零角强度 I(0) i0	4059110000.00
分子量 molecular_weight	534410.0 kDa
排除体积 excluded_volume	667270 Å³
包络体积 envelope_volume	811090 Å³
水化壳体积 shell_volume	130440 Å³
包络直径 envelope_diameter	138.0 Å
壳层 Rg shell_rg	60.13 Å
包络 Rg envelope_rg	46.38 Å
形状 Rg shape_rg	46.63 Å
总 Rg total_rg	46.99 Å
总原子数 total_atoms	37648
残基数 n_residues	4712
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	140.0 Å
Rg (实空间) rg_real	46.85 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	4.0590e+09
I(0) 误差 (实空间) i0_real_error	6.7970e+07
Rg (倒空间) rg_reciprocal	47.33 Å
I(0) (倒空间) i0_reciprocal	4062000000.0000
解质量估计 total_estimate	0.8860
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	63.6 Å
偏度 Skewness skewness	-0.026
峰度 Kurtosis kurtosis	-0.574
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3044000000.0000
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: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.828

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

▶

6. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
分子量 formula_weight	52849.7 kDa
EC 编号 ec_number	4.1.1.39
来源方法 src_method	nat
拷贝数 entity_count	8

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	B,E,H,K,L,O,R,V
原子数 atom_count	40436

MSPQTETKASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV

实体 2 Entity 2 polymer

描述 description	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
分子量 formula_weight	14638.7 kDa
EC 编号 ec_number	4.1.1.39
来源方法 src_method	nat
拷贝数 entity_count	8

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	C,F,I,M,P,S,T,W

MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKPAGY

实体 3 Entity 3 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 4 Entity 4 non-polymer

描述 description	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
分子量 formula_weight	356.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

实体 5 Entity 5 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	2788

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7. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

结构域编号 domain_id	d1upmb1
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.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

结构域编号 domain_id	d1upmb2
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	d1upmc_
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	d1upme1
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.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

结构域编号 domain_id	d1upme2
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	d1upmf_
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	d1upmh1
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.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

结构域编号 domain_id	d1upmh2
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	d1upmi_
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	d1upmk1
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.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

结构域编号 domain_id	d1upmk2
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	d1upml1
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.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

结构域编号 domain_id	d1upml2
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	d1upmm_
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	d1upmo1
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.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

结构域编号 domain_id	d1upmo2
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	d1upmp_
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	d1upmr1
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.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

结构域编号 domain_id	d1upmr2
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	d1upms_
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	d1upmt_
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	d1upmv1
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.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

结构域编号 domain_id	d1upmv2
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	d1upmw_
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	1upmB01
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	1upmB02
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	1upmC00
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	1upmE01
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	1upmE02
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	1upmF00
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	1upmH01
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	1upmH02
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	1upmI00
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	1upmK01
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	1upmK02
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	1upmL01
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	1upmL02
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	1upmM00
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	1upmO01
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	1upmO02
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	1upmP00
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	1upmR01
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	1upmR02
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	1upmS00
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	1upmT00
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	1upmV01
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	1upmV02
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	1upmW00
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

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8. 引用文献 (1)

▶

晶胞边长 a length_a	219.600 Å
晶胞边长 b length_b	220.942 Å
晶胞边长 c length_c	116.984 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	32

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2300
R_free r_free	0.2000

ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.

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 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 (5)

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 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/up/1upm/1upm.fit
pddf	/app/data/pr_computation/up/1upm/1upm.pr.out
profile	/app/data/saxs_computation/up/1upm/1upm.dat