2i5n

1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas viridis:Crystals grown by microfluidic technique

Method: X-RAY DIFFRACTION

SAXS 散射曲线 SAXS Profile

暂无 SAXS 图

P(r) 距离分布 P(r) Distribution

暂无 P(r) 图

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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2i5n
沉积日期 deposition_date	2006-08-25
结构标题 title	1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas viridis:Crystals grown by microfluidic technique
关键词 keywords	Photosynthetic reaction center, secondary quinone (QB), microfluidic technique, hybrid, microbatch, plug, PHOTOSYNTHESIS; PHOTOSYNTHESIS
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

该条目暂无 SAXS 数据。

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

该条目暂无 P(r) 分析数据。

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

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5. 实体与聚合体信息 (16)

Entity 1 polymer

描述 description	Photosynthetic reaction center cytochrome c subunit
分子量 formula_weight	37450.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C
原子数 atom_count	11035

CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIKAAAK

Entity 2 polymer

描述 description	Reaction center protein H chain
分子量 formula_weight	28557.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL

Entity 3 polymer

描述 description	Reaction center protein L chain
分子量 formula_weight	30469.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L

ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS

Entity 4 polymer

描述 description	Reaction center protein M chain
分子量 formula_weight	35932.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	M

ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK

Entity 5 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	19

Entity 6 non-polymer

描述 description	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 7 non-polymer

描述 description	HEPTANE-1,2,3-TRIOL
分子量 formula_weight	148.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 8 non-polymer

描述 description	LAURYL DIMETHYLAMINE-N-OXIDE
分子量 formula_weight	229.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 9 non-polymer

描述 description	UNKNOWN LIGAND
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 10 non-polymer

描述 description	FE (II) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 non-polymer

描述 description	BACTERIOCHLOROPHYLL B
分子量 formula_weight	909.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 12 non-polymer

描述 description	BACTERIOPHEOPHYTIN B
分子量 formula_weight	887.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 13 non-polymer

描述 description	MENAQUINONE-9
分子量 formula_weight	785.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 14 non-polymer

描述 description	UBIQUINONE-1
分子量 formula_weight	250.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 15 non-polymer

描述 description	15-cis-1,2-dihydroneurosporene
分子量 formula_weight	540.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 16 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	771

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6. 折叠分类 (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2i5nc_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.138 — Multiheme cytochromes
超家族 Superfamily superfamily	a.138.1 — Multiheme cytochromes
家族 Family family	a.138.1.2 — Photosynthetic reaction centre (cytochrome subunit)

结构域编号 domain_id	d2i5nh1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.41 — PRC-barrel domain
超家族 Superfamily superfamily	b.41.1 — PRC-barrel domain
家族 Family family	b.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain

结构域编号 domain_id	d2i5nh2
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.23 — Single transmembrane helix
超家族 Superfamily superfamily	f.23.10 — Photosystem II reaction centre subunit H, transmembrane region
家族 Family family	f.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region

结构域编号 domain_id	d2i5nl_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
超家族 Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
家族 Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

结构域编号 domain_id	d2i5nm_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.26 — Bacterial photosystem II reaction centre, L and M subunits
超家族 Superfamily superfamily	f.26.1 — Bacterial photosystem II reaction centre, L and M subunits
家族 Family family	f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits

CATH v4.4 (8 domains)

结构域编号 domain_id	2i5nC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	468 — Photosynthetic Reaction Center, subunit C; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit C, domain 2

结构域编号 domain_id	2i5nC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	468 — Photosynthetic Reaction Center, subunit C; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit C, domain 2

结构域编号 domain_id	2i5nH01
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	540 — Photosynthetic Reaction Center; Chain H, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Photosynthetic reaction centre, H subunit, N-terminal domain

结构域编号 domain_id	2i5nH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	50 — Photosynthetic Reaction Center; Chain H, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Photosynthetic Reaction Center, subunit H, domain 2

结构域编号 domain_id	2i5nL01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Photosystem II protein D1-like

结构域编号 domain_id	2i5nL02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Photosystem II protein D1-like

结构域编号 domain_id	2i5nM01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Photosystem II protein D1-like

结构域编号 domain_id	2i5nM02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	85 — Photosynthetic Reaction Center, subunit M; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Photosystem II protein D1-like

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7. 引用文献 (1)

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晶胞边长 a length_a	220.400 Å
晶胞边长 b length_b	220.400 Å
晶胞边长 c length_c	113.009 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 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	1.960 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1730
R_work r_work	0.1720
R_free r_free	0.1900

1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas viridis:Crystals grown by microfluidic technique

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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

5. 实体与聚合体信息 (16)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 non-polymer

Entity 16 water

6. 折叠分类 (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (0)