SAXSdb — 1jsr

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jsr
沉积日期 deposition_date	2001-08-17
结构标题 title	CRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXED WITH 6-HYDROXY-L-NORLEUCINE
关键词 keywords	ASPARAGINASE, HYDROLASE, COVALENT COMPLEX, 6-DIAZO-5-OXO-L-NORLEUCINE; HYDROLASE
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	30.15 Å
回转半径 Rg (电子) rg_electron	29.27 Å
零角强度 I(0) i0	307076000.00
分子量 molecular_weight	140270.0 kDa
排除体积 excluded_volume	176000 Å³
包络体积 envelope_volume	200460 Å³
水化壳体积 shell_volume	52802 Å³
包络直径 envelope_diameter	92.9 Å
壳层 Rg shell_rg	39.46 Å
包络 Rg envelope_rg	29.45 Å
形状 Rg shape_rg	29.24 Å
总 Rg total_rg	30.19 Å
总原子数 total_atoms	9852
残基数 n_residues	1296
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	89.7 Å
Rg (实空间) rg_real	29.92 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	3.0710e+08
I(0) 误差 (实空间) i0_real_error	4.2540e+06
Rg (倒空间) rg_reciprocal	30.02 Å
I(0) (倒空间) i0_reciprocal	307100000.0000
解质量估计 total_estimate	0.9030
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	38.9 Å
偏度 Skewness skewness	0.076
峰度 Kurtosis kurtosis	-0.546
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	294600000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.958

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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 (5)

Entity 1 polymer

描述 description	L-asparaginase
分子量 formula_weight	35123.0 kDa
EC 编号 ec_number	3.5.1.1
来源方法 src_method	nat
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	11357

ADKLPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY

Entity 2 non-polymer

描述 description	6-HYDROXY-L-NORLEUCINE
分子量 formula_weight	147.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	PENTAETHYLENE GLYCOL
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	1083

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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	d1jsra_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.88 — Glutaminase/Asparaginase
超家族 Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
家族 Family family	c.88.1.1 — Glutaminase/Asparaginase

结构域编号 domain_id	d1jsrb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.88 — Glutaminase/Asparaginase
超家族 Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
家族 Family family	c.88.1.1 — Glutaminase/Asparaginase

结构域编号 domain_id	d1jsrc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.88 — Glutaminase/Asparaginase
超家族 Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
家族 Family family	c.88.1.1 — Glutaminase/Asparaginase

结构域编号 domain_id	d1jsrd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.88 — Glutaminase/Asparaginase
超家族 Superfamily superfamily	c.88.1 — Glutaminase/Asparaginase
家族 Family family	c.88.1.1 — Glutaminase/Asparaginase

CATH v4.4 (8 domains)

结构域编号 domain_id	1jsrA01
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	1170 — L-asparaginase, N-terminal domain

结构域编号 domain_id	1jsrA02
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	40 —

结构域编号 domain_id	1jsrB01
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	1170 — L-asparaginase, N-terminal domain

结构域编号 domain_id	1jsrB02
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	40 —

结构域编号 domain_id	1jsrC01
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	1170 — L-asparaginase, N-terminal domain

结构域编号 domain_id	1jsrC02
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	40 —

结构域编号 domain_id	1jsrD01
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	1170 — L-asparaginase, N-terminal domain

结构域编号 domain_id	1jsrD02
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	40 —

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7. 引用文献 (3)

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晶胞边长 a length_a	106.065 Å
晶胞边长 b length_b	90.361 Å
晶胞边长 c length_c	127.406 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.35 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1900
R_work r_work	0.1825
R_free r_free	0.2094

fit	/app/data/saxs_computation/js/1jsr/1jsr.fit
pddf	/app/data/pr_computation/js/1jsr/1jsr.pr.out
profile	/app/data/saxs_computation/js/1jsr/1jsr.dat

CRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXED WITH 6-HYDROXY-L-NORLEUCINE

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