SAXSdb — 1rf5

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1rf5
沉积日期 deposition_date	2003-11-07
结构标题 title	Structural Studies of Streptococcus pneumoniae EPSP Synthase in Unliganded State
关键词 keywords	shikimate pathway, EPSP synthase, S3P, Glyphosate, PEP, S. pneumoniae, TRANSFERASE; TRANSFERASE
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	36.88 Å
回转半径 Rg (电子) rg_electron	35.89 Å
零角强度 I(0) i0	500220000.00
分子量 molecular_weight	183260.0 kDa
排除体积 excluded_volume	230800 Å³
包络体积 envelope_volume	297560 Å³
水化壳体积 shell_volume	66058 Å³
包络直径 envelope_diameter	121.0 Å
壳层 Rg shell_rg	44.29 Å
包络 Rg envelope_rg	35.71 Å
形状 Rg shape_rg	35.89 Å
总 Rg total_rg	36.45 Å
总原子数 total_atoms	12848
残基数 n_residues	1708
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	112.9 Å
Rg (实空间) rg_real	36.66 Å
Rg 误差 (实空间) rg_real_error	0.80 Å
I(0) (实空间) i0_real	5.0020e+08
I(0) 误差 (实空间) i0_real_error	7.6660e+06
Rg (倒空间) rg_reciprocal	36.80 Å
I(0) (倒空间) i0_reciprocal	500300000.0000
解质量估计 total_estimate	0.8943
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	49.9 Å
偏度 Skewness skewness	0.157
峰度 Kurtosis kurtosis	-0.425
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	256600000.0000
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: 0.920; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.885

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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 (2)

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1rf5a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1rf5b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1rf5c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

结构域编号 domain_id	d1rf5d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.68 — IF3-like
超家族 Superfamily superfamily	d.68.2 — EPT/RTPC-like
家族 Family family	d.68.2.2 — Enolpyruvate transferase, EPT

CATH v4.4 (8 domains)

结构域编号 domain_id	1rf5A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1rf5A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1rf5B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1rf5B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1rf5C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1rf5C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1rf5D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

结构域编号 domain_id	1rf5D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	65 — Alpha-beta prism
拓扑 Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
同源超家族 H-superfamily homologous superfamily	10 — Enolpyruvate transferase domain

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7. 引用文献 (1)

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晶胞边长 a length_a	115.592 Å
晶胞边长 b length_b	116.482 Å
晶胞边长 c length_c	176.323 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2209
R_work r_work	0.2180
R_free r_free	0.2770

描述 description	5-enolpyruvylshikimate-3-phosphate synthase
分子量 formula_weight	45878.8 kDa
EC 编号 ec_number	2.5.1.19
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	13615

Structural Studies of Streptococcus pneumoniae EPSP Synthase in Unliganded State

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Streptococcus pneumoniae
NCBI 分类编号 ncbi_taxonomy_id	1313
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	767

fit	/app/data/saxs_computation/rf/1rf5/1rf5.fit
pddf	/app/data/pr_computation/rf/1rf5/1rf5.pr.out
profile	/app/data/saxs_computation/rf/1rf5/1rf5.dat