SAXSdb — 1ylh

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ylh
沉积日期 deposition_date	2005-01-19
结构标题 title	Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes in Complex with Manganese and Pyruvate
关键词 keywords	PHOSPHOENOLPYRUVATE CARBOXYKINASE, DISULPHIDE BOND, BOUND SULFHYDRL REDUCING AGENT, LYASE; LYASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	24.52 Å
回转半径 Rg (电子) rg_electron	23.58 Å
零角强度 I(0) i0	55771300.00
分子量 molecular_weight	57995.0 kDa
排除体积 excluded_volume	72462 Å³
包络体积 envelope_volume	83778 Å³
水化壳体积 shell_volume	29030 Å³
包络直径 envelope_diameter	81.6 Å
壳层 Rg shell_rg	31.32 Å
包络 Rg envelope_rg	23.76 Å
形状 Rg shape_rg	23.57 Å
总 Rg total_rg	24.46 Å
总原子数 total_atoms	4077
残基数 n_residues	524
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

▼

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

最大尺寸 Dmax dmax	81.0 Å
Rg (实空间) rg_real	24.44 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	5.5770e+07
I(0) 误差 (实空间) i0_real_error	7.1510e+05
Rg (倒空间) rg_reciprocal	24.46 Å
I(0) (倒空间) i0_reciprocal	55770000.0000
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	29.6 Å
偏度 Skewness skewness	0.295
峰度 Kurtosis kurtosis	-0.311
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20970000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.983

▶

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

▶

5. 实体与聚合体信息 (8)

Entity 1 polymer

描述 description	phosphoenolpyruvate carboxykinase
分子量 formula_weight	61895.7 kDa
EC 编号 ec_number	4.1.1.49
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	A
原子数 atom_count	4274

MGHHHHHHDYDIPTTENLYFQGMTDLNKLVKELNDLGLTDVKEIVYNPSYEQLFEEETKPGLEGFDKGTLTTLGAVAVDTGIFTGRSPKDKYIVCDETTKDTVWWNSEAAKNDNKPMTQETWKSLRELVAKQLSGKRLFVVEGYCGASEKHRIGVRMVTEVAWQAHFVKNMFIRPTDEELKNFKADFTVLNGAKCTNPNWKEQGLNSENFVAFNITEGIQLIGGTWYGGEMKKGMFSMMNYFLPLKGVASMHCSANVGKDGDVAIFFGLSGTGKTTLSTDPKRQLIGDDEHGWDESGVFNFEGGCYAKTINLSQENEPDIYGAIRRDALLENVVVRADGSVDFDDGSKTENTRVSYPIYHIDNIVRPVSKAGHATKVIFLTADAFGVLPPVSKLTPEQTEYYFLSGFTAKLAGTERGVTEPTPTFSACFGAAFLSLHPIQYADVLVERMKASGAEAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIEKAEMGELPIFNLAIPKALPGVDPAILDPRDTYADKAQWQVKAEDLANRFVKNFVKYTANPEAAKLVGAGPKA

来源 Source

来源生物 organism	Actinobacillus succinogenes
NCBI 分类编号 ncbi_taxonomy_id	67854
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	(2S,3S)-2,3-DIHYDROXY-4-SULFANYLBUTANE-1-SULFONATE
分子量 formula_weight	201.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	BETA-MERCAPTOETHANOL
分子量 formula_weight	78.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	PYRUVIC ACID
分子量 formula_weight	88.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	FORMIC ACID
分子量 formula_weight	46.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 8 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	197

▼

6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ylha1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.109 — PEP carboxykinase N-terminal domain
超家族 Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
家族 Family family	c.109.1.1 — PEP carboxykinase N-terminal domain

结构域编号 domain_id	d1ylha2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.91 — PEP carboxykinase-like
超家族 Superfamily superfamily	c.91.1 — PEP carboxykinase-like
家族 Family family	c.91.1.1 — PEP carboxykinase C-terminal domain

CATH v4.4 (3 domains)

结构域编号 domain_id	1ylhA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

结构域编号 domain_id	1ylhA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

结构域编号 domain_id	1ylhA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
同源超家族 H-superfamily homologous superfamily	20 —

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	56.737 Å
晶胞边长 b length_b	55.089 Å
晶胞边长 c length_c	90.077 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.17 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

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	1.700 Å
最低分辨率 resolution_low	26.260 Å
R 因子 r_factor	0.1950
R_work r_work	0.1900
R_free r_free	0.2150

fit	/app/data/saxs_computation/yl/1ylh/1ylh.fit
pddf	/app/data/pr_computation/yl/1ylh/1ylh.pr.out
profile	/app/data/saxs_computation/yl/1ylh/1ylh.dat

Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes in Complex with Manganese and Pyruvate

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution