1s5l

Architecture of the photosynthetic oxygen evolving center

Method: X-RAY DIFFRACTION Dmax: 197.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1s5l

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1s5l
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1s5l
沉积日期 deposition_date2004-01-21
结构标题 titleArchitecture of the photosynthetic oxygen evolving center
关键词 keywordsphotosystem, photosynthesis, oxygen-evolving, tetra-manganese, membrane; PHOTOSYNTHESIS
实验方法 methodX-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier57.60
回转半径 Rg (电子) rg_electron57.38
零角强度 I(0) i04264800000.00
分子量 molecular_weight646650.0 kDa
排除体积 excluded_volume844590 ų
包络体积 envelope_volume1099400 ų
水化壳体积 shell_volume150790 ų
包络直径 envelope_diameter209.9
壳层 Rg shell_rg64.79
包络 Rg envelope_rg57.56
形状 Rg shape_rg57.36
总 Rg total_rg57.65
总原子数 total_atoms45945
残基数 n_residues5130
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

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

最大尺寸 Dmax dmax197.5
Rg (实空间) rg_real57.53
Rg 误差 (实空间) rg_real_error1.71
I(0) (实空间) i0_real4.2650e+09
I(0) 误差 (实空间) i0_real_error7.9540e+07
Rg (倒空间) rg_reciprocal57.64
I(0) (倒空间) i0_reciprocal4265000000.0000
解质量估计 total_estimate0.8603
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary65.8
偏度 Skewness skewness0.351
峰度 Kurtosis kurtosis-0.294
角度范围 angular_range— – 0.1350 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha964500000.0000
实空间数据点数 n_real_points28
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.801

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

5. 实体与聚合体信息 (28)

6. 折叠分类 (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

结构域编号 domain_id1s5lB02
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology680 — Photosystem II CP47 reaction center protein
同源超家族 H-superfamily homologous superfamily10 — Photosystem II CP47 reaction center protein
结构域编号 domain_id1s5lC02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily670 — photosystem ii from thermosynechococcus elongatus
结构域编号 domain_id1s5lE00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily860 — Photosystem II cytochrome b559, alpha subunit
结构域编号 domain_id1s5lH00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily880 — Photosystem II reaction center protein H
结构域编号 domain_id1s5lO01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology160 — Porin
同源超家族 H-superfamily homologous superfamily30 — Photosystem II, cytochrome c-550 precursor
结构域编号 domain_id1s5lO02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2050 — photosynthetic oxygen evolving center fold
同源超家族 H-superfamily homologous superfamily10 — photosynthetic oxygen evolving center domain
结构域编号 domain_id1s5lU01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily320 — Photosystem II 12 kDa extrinsic protein
结构域编号 domain_id1s5lV00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c-like domain
结构域编号 domain_id1s5lX00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily510 — Single helix bin
结构域编号 domain_id1s5lZ00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily740 — Photosystem II PsbZ, reaction centre
结构域编号 domain_id1s5lb02
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology680 — Photosystem II CP47 reaction center protein
同源超家族 H-superfamily homologous superfamily10 — Photosystem II CP47 reaction center protein
结构域编号 domain_id1s5lc02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily670 — photosystem ii from thermosynechococcus elongatus
结构域编号 domain_id1s5le00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily860 — Photosystem II cytochrome b559, alpha subunit
结构域编号 domain_id1s5lh00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily880 — Photosystem II reaction center protein H
结构域编号 domain_id1s5lo01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology160 — Porin
同源超家族 H-superfamily homologous superfamily30 — Photosystem II, cytochrome c-550 precursor
结构域编号 domain_id1s5lo02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology2050 — photosynthetic oxygen evolving center fold
同源超家族 H-superfamily homologous superfamily10 — photosynthetic oxygen evolving center domain
结构域编号 domain_id1s5lu01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology150 — DNA polymerase; domain 1
同源超家族 H-superfamily homologous superfamily320 — Photosystem II 12 kDa extrinsic protein
结构域编号 domain_id1s5lv00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c-like domain
结构域编号 domain_id1s5lx00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily510 — Single helix bin
结构域编号 domain_id1s5lz00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily740 — Photosystem II PsbZ, reaction centre

7. 引用文献 (1)

8. 文件与曲线 (10)