5tuw

Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore

Method: X-RAY DIFFRACTION

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

Orange carotenoid-binding protein

Synechocystis sp. (strain PCC 6803 / Kazusa)

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	蛋白同源多聚体	同源多聚体	蛋白 6	GLYCEROL × 4 (3'R)-3'-hydroxy-beta,beta-caroten-4-one × 6 water × 6	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	OCP_SYNY3
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–317； UniProt 1–317 作者链 B； PDB构建体 1–317； UniProt 1–317 作者链 C； PDB构建体 1–317； UniProt 1–317 作者链 D； PDB构建体 1–317； UniProt 1–317 作者链 E； PDB构建体 1–317； UniProt 1–317 作者链 F； PDB构建体 1–317； UniProt 1–317

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。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	5tuw
沉积日期 deposition_date	2016-11-07
结构标题 title	Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore
关键词 keywords	Photoreceptor, Photoprotection, Dynamic crystallography, Carotenoid binding protein; Carotenoid binding protein
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

5tuw__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

5tuw__assembly_1__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

5tuw__assembly_1__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	42.05 Å
Rg（电子密度）	41.60 Å
总 Rg	41.90 Å
原子数	14715
残基数	1830
排除体积	258250 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`5tuw__assembly_1__model_1`	hexameric （6）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	Orange carotenoid-binding protein
分子量 formula_weight	35513.5 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	15054

MPFTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTAGKDGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKELLNFARHHHHHH

来源 Source

来源生物 organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI 分类编号 ncbi_taxonomy_id	1111708
宿主生物 host_organism	Synechocystis sp. PCC 6803

实体 2 Entity 2 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 3 Entity 3 non-polymer

描述 description	(3'R)-3'-hydroxy-beta,beta-caroten-4-one
分子量 formula_weight	566.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	263

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d5tuwa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
超家族 Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
家族 Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

结构域编号 domain_id	d5tuwa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.0 — automated matches

结构域编号 domain_id	d5tuwb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
超家族 Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
家族 Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

结构域编号 domain_id	d5tuwb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.0 — automated matches

结构域编号 domain_id	d5tuwc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
超家族 Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
家族 Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

结构域编号 domain_id	d5tuwc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.0 — automated matches

结构域编号 domain_id	d5tuwd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
超家族 Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
家族 Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

结构域编号 domain_id	d5tuwd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.0 — automated matches

结构域编号 domain_id	d5tuwe1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
超家族 Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
家族 Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

结构域编号 domain_id	d5tuwe2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.0 — automated matches

结构域编号 domain_id	d5tuwf1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.175 — Orange carotenoid protein, N-terminal domain
超家族 Superfamily superfamily	a.175.1 — Orange carotenoid protein, N-terminal domain
家族 Family family	a.175.1.1 — Orange carotenoid protein, N-terminal domain

结构域编号 domain_id	d5tuwf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.17 — Cystatin-like
超家族 Superfamily superfamily	d.17.4 — NTF2-like
家族 Family family	d.17.4.0 — automated matches

CATH v4.4 (12 domains)

结构域编号 domain_id	5tuwA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2090 — orange carotenoid protein, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

结构域编号 domain_id	5tuwA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	5tuwB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2090 — orange carotenoid protein, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

结构域编号 domain_id	5tuwB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	5tuwC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2090 — orange carotenoid protein, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

结构域编号 domain_id	5tuwC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	5tuwD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2090 — orange carotenoid protein, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

结构域编号 domain_id	5tuwD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	5tuwE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2090 — orange carotenoid protein, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

结构域编号 domain_id	5tuwE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	5tuwF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2090 — orange carotenoid protein, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Orange carotenoid-binding protein, N-terminal domain

结构域编号 domain_id	5tuwF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	50 —

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晶胞边长 a length_a	82.947 Å
晶胞边长 b length_b	82.914 Å
晶胞边长 c length_c	87.438 Å
晶胞夹角 α angle_alpha	89.79 °
晶胞夹角 β angle_beta	89.91 °
晶胞夹角 γ angle_gamma	60.04 °
晶胞分子数 Z z_pdb	6

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

分辨率 resolution	2.302 Å
最低分辨率 resolution_low	41.490 Å
R 因子 r_factor	0.1859
R_work r_work	0.1846
R_free r_free	0.2386

Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore

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

Orange carotenoid-binding protein

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

5tuw__assembly_1__model_1

5tuw__assembly_1__model_1 | I(q)

5tuw__assembly_1__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 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 non-polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echinenone chromophore

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

Orange carotenoid-binding protein

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

5tuw__assembly_1__model_1

5tuw__assembly_1__model_1 | I(q)

5tuw__assembly_1__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 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 non-polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)