SAXSdb — 1kl7

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kl7
沉积日期 deposition_date	2001-12-11
结构标题 title	Crystal Structure of Threonine Synthase from Yeast
关键词 keywords	threonine synthesis, pyridoxal 5-phosphate, beta-family, monomer, LYASE; LYASE
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	36.59 Å
回转半径 Rg (电子) rg_electron	36.01 Å
零角强度 I(0) i0	190490000.00
分子量 molecular_weight	113260.0 kDa
排除体积 excluded_volume	142020 Å³
包络体积 envelope_volume	177950 Å³
水化壳体积 shell_volume	40557 Å³
包络直径 envelope_diameter	113.8 Å
壳层 Rg shell_rg	42.90 Å
包络 Rg envelope_rg	35.67 Å
形状 Rg shape_rg	36.00 Å
总 Rg total_rg	36.49 Å
总原子数 total_atoms	7960
残基数 n_residues	1006
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	115.2 Å
Rg (实空间) rg_real	36.66 Å
Rg 误差 (实空间) rg_real_error	0.74 Å
I(0) (实空间) i0_real	1.9050e+08
I(0) 误差 (实空间) i0_real_error	2.8460e+06
Rg (倒空间) rg_reciprocal	36.62 Å
I(0) (倒空间) i0_reciprocal	190500000.0000
解质量估计 total_estimate	0.8069
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.1 Å
偏度 Skewness skewness	0.269
峰度 Kurtosis kurtosis	-0.838
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	42000000.0000
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: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; 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 (3)

Entity 1 polymer

描述 description	Threonine Synthase
分子量 formula_weight	57867.2 kDa
EC 编号 ec_number	4.2.99.2
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	8294

MPNASQVYRSTRSSSPKTISFEEAIIQGLATDGGLFIPPTIPQVDQATLFNDWSKLSFQDLAFAIMRLYIAQEEIPDADLKDLIKRSYSTFRSDEVTPLVQNVTGDKENLHILELFHGPTYAFKDVALQFVGNLFEYFLQRTNANLPEGEKKQITVVGATSGDTGSAAIYGLRGKKDVSVFILYPTGRISPIQEEQMTTVPDENVQTLSVTGTFDNCQDIVKAIFGDKEFNSKHNVGAVNSINWARILAQMTYYFYSFFQATNGKDSKKVKFVVPSGNFGDILAGYFAKKMGLPIEKLAIATNENDILDRFLKSGLYERSDKVAATLSPAMDILISSNFERLLWYLAREYLANGDDLKAGEIVNNWFQELKTNGKFQVDKSIIEGASKDFTSERVSNEETSETIKKIYESSVNPKHYILDPHTAVGVCATERLIAKDNDKSIQYISLSTAHPAKFADAVNNALSGFSNYSFEKDVLPEELKKLSTLKKKLKFIERADVELVKNAIEEELAKMKL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	PYRIDOXAL-5'-PHOSPHATE
分子量 formula_weight	247.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	334

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1kl7a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
超家族 Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
家族 Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

结构域编号 domain_id	d1kl7b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
超家族 Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
家族 Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

CATH v4.4 (6 domains)

结构域编号 domain_id	1kl7A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1380 — threonine synthase, domain 1, chain A
同源超家族 H-superfamily homologous superfamily	10 — Threonine synthase, N-terminal domain

结构域编号 domain_id	1kl7A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1100 —

结构域编号 domain_id	1kl7A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1100 —

结构域编号 domain_id	1kl7B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1380 — threonine synthase, domain 1, chain A
同源超家族 H-superfamily homologous superfamily	10 — Threonine synthase, N-terminal domain

结构域编号 domain_id	1kl7B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1100 —

结构域编号 domain_id	1kl7B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1100 —

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7. 引用文献 (1)

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晶胞边长 a length_a	95.300 Å
晶胞边长 b length_b	51.600 Å
晶胞边长 c length_c	106.900 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.60 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.700 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2009
R_free r_free	0.2526

fit	/app/data/saxs_computation/kl/1kl7/1kl7.fit
pddf	/app/data/pr_computation/kl/1kl7/1kl7.pr.out
profile	/app/data/saxs_computation/kl/1kl7/1kl7.dat

Crystal Structure of Threonine Synthase from Yeast

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