2jj0

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M248 REPLACED WITH TRP (CHAIN M, AM248W)

Method: X-RAY DIFFRACTION D_max: 88.5 Å Quality: EXCELLENT

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	2jj0
沉积日期 deposition_date	2007-07-03
结构标题 title	PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M248 REPLACED WITH TRP (CHAIN M, AM248W)
关键词 keywords	;PHOTOSYNTHESIS, REACTION CENTER, MEMBRANE PROTEIN, PHOTOSYNTHETIC REACTION CENTER, ELECTRON TRANSPORT, BACTERIOCHLOROPHYLL, CHLOROPHYLL, METAL-BINDING, TRANSMEMBRANE, IRON, MEMBRANE, TRANSPORT, MAGNESIUM, CHROMOPHORE ;; 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	29.49 Å
回转半径 Rg (电子) rg_electron	28.26 Å
零角强度 I(0) i0	120264000.00
分子量 molecular_weight	98113.0 kDa
排除体积 excluded_volume	127150 Å³
包络体积 envelope_volume	143830 Å³
水化壳体积 shell_volume	40734 Å³
包络直径 envelope_diameter	94.2 Å
壳层 Rg shell_rg	36.91 Å
包络 Rg envelope_rg	28.47 Å
形状 Rg shape_rg	28.26 Å
总 Rg total_rg	29.15 Å
总原子数 total_atoms	6968
残基数 n_residues	817
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	88.5 Å
Rg (实空间) rg_real	29.37 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	1.2030e+08
I(0) 误差 (实空间) i0_real_error	1.6730e+06
Rg (倒空间) rg_reciprocal	29.42 Å
I(0) (倒空间) i0_reciprocal	120300000.0000
解质量估计 total_estimate	0.9087
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	36.0 Å
偏度 Skewness skewness	0.166
峰度 Kurtosis kurtosis	-0.554
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14030000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.977; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.881

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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	REACTION CENTER PROTEIN H CHAIN
分子量 formula_weight	28066.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H
原子数 atom_count	7111

MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKSVVAAMLAEYA

来源 Source

来源生物 organism	RHODOBACTER SPHAEROIDES
NCBI 分类编号 ncbi_taxonomy_id	1063
宿主生物 host_organism	RHODOBACTER SPHAEROIDES

Entity 2 polymer

描述 description	REACTION CENTER PROTEIN L CHAIN
分子量 formula_weight	31346.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

来源 Source

来源生物 organism	RHODOBACTER SPHAEROIDES
NCBI 分类编号 ncbi_taxonomy_id	1063
宿主生物 host_organism	RHODOBACTER SPHAEROIDES

Entity 3 polymer

描述 description	REACTION CENTER PROTEIN M CHAIN
分子量 formula_weight	34644.9 kDa
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

MAEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERWALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLN

来源 Source

来源生物 organism	RHODOBACTER SPHAEROIDES
NCBI 分类编号 ncbi_taxonomy_id	1063
宿主生物 host_organism	RHODOBACTER SPHAEROIDES

Entity 4 non-polymer

描述 description	BACTERIOCHLOROPHYLL A
分子量 formula_weight	911.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	BACTERIOPHEOPHYTIN A
分子量 formula_weight	889.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	UBIQUINONE-10
分子量 formula_weight	863.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	CARDIOLIPIN
分子量 formula_weight	1464.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

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

Entity 9 non-polymer

描述 description	SPEROIDENONE
分子量 formula_weight	595.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	122

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2jj0h1
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	d2jj0h2
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	d2jj0l_
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	d2jj0m_
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 (6 domains)

结构域编号 domain_id	2jj0H01
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	2jj0H02
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	2jj0L01
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	2jj0L02
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	2jj0M01
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	2jj0M02
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 (4)

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晶胞边长 a length_a	139.810 Å
晶胞边长 b length_b	139.810 Å
晶胞边长 c length_c	185.153 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	6

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	27.900 Å
R 因子 r_factor	0.2050
R_work r_work	0.2030
R_free r_free	0.2450

fit	/app/data/saxs_computation/jj/2jj0/2jj0.fit
pddf	/app/data/pr_computation/jj/2jj0/2jj0.pr.out
profile	/app/data/saxs_computation/jj/2jj0/2jj0.dat

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M248 REPLACED WITH TRP (CHAIN M, AM248W)

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 (11)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-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 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)