1rwt

Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution

Method: X-RAY DIFFRACTION D_max: 182.4 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	1rwt
沉积日期 deposition_date	2003-12-17
结构标题 title	Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution
关键词 keywords	LIGHT-HARVESTING COMPLEX, MEMBRANE PROTEIN, PLANT, 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	63.99 Å
回转半径 Rg (电子) rg_electron	63.44 Å
零角强度 I(0) i0	1070360000.00
分子量 molecular_weight	396470.0 kDa
排除体积 excluded_volume	540610 Å³
包络体积 envelope_volume	718990 Å³
水化壳体积 shell_volume	92494 Å³
包络直径 envelope_diameter	204.1 Å
壳层 Rg shell_rg	67.57 Å
包络 Rg envelope_rg	61.25 Å
形状 Rg shape_rg	63.44 Å
总 Rg total_rg	63.57 Å
总原子数 total_atoms	28340
残基数 n_residues	2181
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	182.4 Å
Rg (实空间) rg_real	64.00 Å
Rg 误差 (实空间) rg_real_error	1.07 Å
I(0) (实空间) i0_real	1.0700e+09
I(0) 误差 (实空间) i0_real_error	2.0600e+07
Rg (倒空间) rg_reciprocal	63.89 Å
I(0) (倒空间) i0_reciprocal	1070000000.0000
解质量估计 total_estimate	0.8285
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	102.2 Å
偏度 Skewness skewness	0.138
峰度 Kurtosis kurtosis	-0.841
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0005
最高正则化参数 α highest_alpha	264700000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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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 (11)

Entity 1 polymer

描述 description	Chlorophyll A-B binding protein, chloroplast
分子量 formula_weight	25000.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	29039

RKTAGKPKTVQSSSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWNFATNFVPGK

Entity 2 non-polymer

描述 description	nonyl beta-D-glucopyranoside
分子量 formula_weight	306.4 kDa
来源方法 src_method	man
拷贝数 entity_count	10

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
分子量 formula_weight	568.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

Entity 5 non-polymer

描述 description	;(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL ;
分子量 formula_weight	600.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 6 non-polymer

描述 description	;(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL ;
分子量 formula_weight	600.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 7 non-polymer

描述 description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
分子量 formula_weight	723.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 8 non-polymer

描述 description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
分子量 formula_weight	949.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 9 non-polymer

描述 description	CHLOROPHYLL B
分子量 formula_weight	907.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	60

Entity 10 non-polymer

描述 description	CHLOROPHYLL A
分子量 formula_weight	893.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	80

Entity 11 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	699

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1rwta_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwtb_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwtc_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwtd_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwte_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwtf_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwtg_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwth_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwti_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

结构域编号 domain_id	d1rwtj_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.43 — Chlorophyll a-b binding protein
超家族 Superfamily superfamily	f.43.1 — Chlorophyll a-b binding protein
家族 Family family	f.43.1.1 — Chlorophyll a-b binding protein

CATH v4.4 (10 domains)

结构域编号 domain_id	1rwtA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtI01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

结构域编号 domain_id	1rwtJ01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	3460 — Chlorophyll a-b binding protein
同源超家族 H-superfamily homologous superfamily	10 — Chlorophyll a/b binding protein domain

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7. 引用文献 (1)

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晶胞边长 a length_a	261.787 Å
晶胞边长 b length_b	261.787 Å
晶胞边长 c length_c	660.498 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	120.00 °
晶胞分子数 Z z_pdb	180

空间群 space_group	H 3 2
空间群编号 int_tables_number	155
晶系 crystal_system	—

分辨率 resolution	2.720 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2210

fit	/app/data/saxs_computation/rw/1rwt/1rwt.fit
pddf	/app/data/pr_computation/rw/1rwt/1rwt.pr.out
profile	/app/data/saxs_computation/rw/1rwt/1rwt.dat