1vrn

PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)

Method: X-RAY DIFFRACTION D_max: 125.2 Å Quality: GOOD

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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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1vrn
沉积日期 deposition_date	2005-02-23
结构标题 title	PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)
关键词 keywords	INTEGRAL MEMBRANE PROTEIN; UBIQUINONE; SECONDARY QUINONE (QB), 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)

回转半径 Rg (Guinier) rg_guinier	36.83 Å
回转半径 Rg (电子) rg_electron	35.80 Å
零角强度 I(0) i0	262124000.00
分子量 molecular_weight	143920.0 kDa
排除体积 excluded_volume	184820 Å³
包络体积 envelope_volume	213720 Å³
水化壳体积 shell_volume	50313 Å³
包络直径 envelope_diameter	135.4 Å
壳层 Rg shell_rg	41.55 Å
包络 Rg envelope_rg	36.41 Å
形状 Rg shape_rg	35.72 Å
总 Rg total_rg	36.46 Å
总原子数 total_atoms	10191
残基数 n_residues	1185
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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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	125.2 Å
Rg (实空间) rg_real	37.08 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	2.6210e+08
I(0) 误差 (实空间) i0_real_error	4.6990e+06
Rg (倒空间) rg_reciprocal	36.93 Å
I(0) (倒空间) i0_reciprocal	262100000.0000
解质量估计 total_estimate	0.8432
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.9 Å
偏度 Skewness skewness	0.541
峰度 Kurtosis kurtosis	-0.138
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	47610000.0000
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: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.651

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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 (14)

Entity 1 polymer

描述 description	Photosynthetic reaction center cytochrome c subunit
分子量 formula_weight	37108.4 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	10747

CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIK

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

Entity 6 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	7

Entity 7 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	6

Entity 8 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 9 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 10 non-polymer

描述 description	UBIQUINONE-7
分子量 formula_weight	659.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 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 12 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 13 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 14 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	542

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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	d1vrnc_
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	d1vrnh1
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	d1vrnh2
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	d1vrnl_
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	d1vrnm_
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	1vrnC01
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	1vrnC02
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	1vrnH01
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	1vrnH02
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	1vrnL01
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	1vrnL02
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	1vrnM01
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	1vrnM02
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 (2)

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晶胞边长 a length_a	219.400 Å
晶胞边长 b length_b	219.400 Å
晶胞边长 c length_c	112.600 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	2.200 Å
最低分辨率 resolution_low	19.180 Å
R 因子 r_factor	0.1911
R_work r_work	0.1910
R_free r_free	0.2120

fit	/app/data/saxs_computation/vr/1vrn/1vrn.fit
pddf	/app/data/pr_computation/vr/1vrn/1vrn.pr.out
profile	/app/data/saxs_computation/vr/1vrn/1vrn.dat

PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)

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

衍射实验 Diffraction

5. 实体与聚合体信息 (14)

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 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 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)