SAXSdb — 8eu4

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8eu4
沉积日期 deposition_date	2022-10-18
结构标题 title	Escherichia coli pyruvate kinase A301S
关键词 keywords	Pyruvate kinase, Long term evolution experiment, Kinase, 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	78.82 Å
回转半径 Rg (电子) rg_electron	79.96 Å
零角强度 I(0) i0	2268320000.00
分子量 molecular_weight	397750.0 kDa
排除体积 excluded_volume	497160 Å³
包络体积 envelope_volume	785070 Å³
水化壳体积 shell_volume	88678 Å³
包络直径 envelope_diameter	268.8 Å
壳层 Rg shell_rg	64.35 Å
包络 Rg envelope_rg	77.97 Å
形状 Rg shape_rg	79.97 Å
总 Rg total_rg	79.69 Å
总原子数 total_atoms	56233
残基数 n_residues	3695
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	224.7 Å
Rg (实空间) rg_real	77.37 Å
Rg 误差 (实空间) rg_real_error	1.38 Å
I(0) (实空间) i0_real	2.2360e+09
I(0) 误差 (实空间) i0_real_error	4.7890e+07
Rg (倒空间) rg_reciprocal	75.20 Å
I(0) (倒空间) i0_reciprocal	2246000000.0000
解质量估计 total_estimate	0.8177
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	56.2 Å
偏度 Skewness skewness	0.451
峰度 Kurtosis kurtosis	-0.741
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.0934
最高正则化参数 α highest_alpha	56590000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 0.981; Sysdev: 1.000; Positv: 1.000; Valcen: 0.881; Smooth: 0.273

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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	Pyruvate kinase
分子量 formula_weight	50808.3 kDa
EC 编号 ec_number	2.7.1.40
突变 mutation	A301S
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,E,D,G,B,F,H,C
原子数 atom_count	57299

MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVMSKTGKTAAILLDTKGPEIRTMKLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGLIGMEVTAIEGNKVICKVLNNGDLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIREHLKAHGGENIHIISKIENQEGLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQMLDSMIKNPRPTRAEAGDVANSILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEFNNDNRKLRITEAVCRGAVETAEKLDAPLIVVATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHKGDVVVMVSGALVPSGTTNTASVHVL

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	1066

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	8eu4A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	33 — M1 Pyruvate Kinase; Domain 3
同源超家族 H-superfamily homologous superfamily	10 — PK beta-barrel domain-like

结构域编号 domain_id	8eu4B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	33 — M1 Pyruvate Kinase; Domain 3
同源超家族 H-superfamily homologous superfamily	10 — PK beta-barrel domain-like

结构域编号 domain_id	8eu4C01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	33 — M1 Pyruvate Kinase; Domain 3
同源超家族 H-superfamily homologous superfamily	10 — PK beta-barrel domain-like

结构域编号 domain_id	8eu4D01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	33 — M1 Pyruvate Kinase; Domain 3
同源超家族 H-superfamily homologous superfamily	10 — PK beta-barrel domain-like

结构域编号 domain_id	8eu4E01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	33 — M1 Pyruvate Kinase; Domain 3
同源超家族 H-superfamily homologous superfamily	10 — PK beta-barrel domain-like

结构域编号 domain_id	8eu4F01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	33 — M1 Pyruvate Kinase; Domain 3
同源超家族 H-superfamily homologous superfamily	10 — PK beta-barrel domain-like

结构域编号 domain_id	8eu4G01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	33 — M1 Pyruvate Kinase; Domain 3
同源超家族 H-superfamily homologous superfamily	10 — PK beta-barrel domain-like

结构域编号 domain_id	8eu4H01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	33 — M1 Pyruvate Kinase; Domain 3
同源超家族 H-superfamily homologous superfamily	10 — PK beta-barrel domain-like

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7. 引用文献 (1)

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晶胞边长 a length_a	129.334 Å
晶胞边长 b length_b	74.473 Å
晶胞边长 c length_c	240.826 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.04 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.100 Å
最低分辨率 resolution_low	48.170 Å
R 因子 r_factor	0.2037
R_work r_work	0.2020
R_free r_free	0.2236

fit	/app/data/saxs_computation/eu/8eu4/8eu4.fit
pddf	/app/data/pr_computation/eu/8eu4/8eu4.pr.out
profile	/app/data/saxs_computation/eu/8eu4/8eu4.dat

Escherichia coli pyruvate kinase A301S

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