SAXSdb — 1rf4

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1rf4
沉积日期 deposition_date	2003-11-07
结构标题 title	Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate Bound 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	38.95 Å
回转半径 Rg (电子) rg_electron	37.83 Å
零角强度 I(0) i0	509069000.00
分子量 molecular_weight	185020.0 kDa
排除体积 excluded_volume	232380 Å³
包络体积 envelope_volume	294230 Å³
水化壳体积 shell_volume	61738 Å³
包络直径 envelope_diameter	116.7 Å
壳层 Rg shell_rg	46.92 Å
包络 Rg envelope_rg	36.76 Å
形状 Rg shape_rg	37.87 Å
总 Rg total_rg	38.21 Å
总原子数 total_atoms	12956
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	111.0 Å
Rg (实空间) rg_real	38.59 Å
Rg 误差 (实空间) rg_real_error	0.70 Å
I(0) (实空间) i0_real	5.0910e+08
I(0) 误差 (实空间) i0_real_error	7.4200e+06
Rg (倒空间) rg_reciprocal	38.82 Å
I(0) (倒空间) i0_reciprocal	509200000.0000
解质量估计 total_estimate	0.8851
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	54.2 Å
偏度 Skewness skewness	-0.071
峰度 Kurtosis kurtosis	-0.651
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	315700000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.665

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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 (3)

Entity 1 polymer

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 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	13729

MKLKTNIRHLHGIIRVPGDKSISHRSIIFGSLAEGETKVYDILRGEDVLSTMQVFRDLGVEIEDKDGVITVQGVGMAGLKAPQNALNMGNSGTSIRLISGVLAGADFEVEMFGDDSLSKRPMDRVTLPLKKMGVSISGQTERDLPPLRLKGTKNLRPIHYELPIASAQVKSALMFAALQAKGESVIIEKEYTRNHTEDMLQQFGGHLSVDGKKITVQGPQKLTGQKVVVPGDISSAAFWLVAGLIAPNSRLVLQNVGINETRTGIIDVIRAMGGKLEITEIDPVAKSATLIVESSDLKGTEICGALIPRLIDELPIIALLATQAQGVTVIKDAEELKVKETDRIQVVADALNSMGADITPTADGMIIKGKSALHGARVNTFGDHRIGMMTAIAALLVADGEVELDRAEAINTSYPSFFDDLESLIHG

来源 Source

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

Entity 2 non-polymer

描述 description	(3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FLUORO-1-(PHOSPHONOOXY)ETHYL]OXY}-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID
分子量 formula_weight	440.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 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	773

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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	d1rf4a_
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	d1rf4b_
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	d1rf4c_
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	d1rf4d_
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	1rf4A01
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	1rf4A02
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	1rf4B01
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	1rf4B02
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	1rf4C01
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	1rf4C02
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	1rf4D01
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	1rf4D02
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	82.495 Å
晶胞边长 b length_b	149.705 Å
晶胞边长 c length_c	88.011 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.22 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2140
R_work r_work	0.1960
R_free r_free	0.2360

fit	/app/data/saxs_computation/rf/1rf4/1rf4.fit
pddf	/app/data/pr_computation/rf/1rf4/1rf4.pr.out
profile	/app/data/saxs_computation/rf/1rf4/1rf4.dat

Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate Bound 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