1njj

Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418

Method: X-RAY DIFFRACTION D_max: 211.3 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1njj
沉积日期 deposition_date	2002-12-31
结构标题 title	Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418
关键词 keywords	;ornithine decarboxylase, ODC, PLP, pyridoxal 5'-phosphate, D-ornithine, G418, 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	65.05 Å
回转半径 Rg (电子) rg_electron	65.87 Å
零角强度 I(0) i0	338235000.00
分子量 molecular_weight	159360.0 kDa
排除体积 excluded_volume	200820 Å³
包络体积 envelope_volume	336430 Å³
水化壳体积 shell_volume	42365 Å³
包络直径 envelope_diameter	197.5 Å
壳层 Rg shell_rg	72.17 Å
包络 Rg envelope_rg	60.72 Å
形状 Rg shape_rg	65.87 Å
总 Rg total_rg	66.00 Å
总原子数 total_atoms	11217
残基数 n_residues	1404
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	211.3 Å
Rg (实空间) rg_real	65.93 Å
Rg 误差 (实空间) rg_real_error	3.18 Å
I(0) (实空间) i0_real	3.3820e+08
I(0) 误差 (实空间) i0_real_error	7.8930e+06
Rg (倒空间) rg_reciprocal	64.09 Å
I(0) (倒空间) i0_reciprocal	337100000.0000
解质量估计 total_estimate	0.5641
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	35.2 Å
偏度 Skewness skewness	0.151
峰度 Kurtosis kurtosis	-1.406
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8823000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.007; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.139; Smooth: 0.170

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	ornithine decarboxylase
分子量 formula_weight	47150.6 kDa
EC 编号 ec_number	4.1.1.17
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	11424

KSMDIVVNDDLSCRFLEGFNTRDALCKKISMNTCDEGDPFFVADLGDIVRKHETWKKCLPRVTPFYAVKCNDDWRVLGTLAALGTGFDCASNTEIQRVRGIGVPPEKIIYANPCKQISHIRYARDSGVDVMTFDCVDELEKVAKTHPKAKMVLRISTDDSLARCRLSVKFGAKVEDCRFILEQAKKLNIDVTGVSFHVGSGSTDASTFAQAISDSRFVFDMGTELGFNMHILDIGGGFPGTRDAPLKFEEIAGVINNALEKHFPPDLKLTIVAEPGRYYVASAFTLAVNVIAKKVTPGVQTDVGAHAESNAQSFMYYVNDGVYGSFNCILYDHAVVRPLPQREPIPNEKLYPSSVWGPTCDGLDQIVERYYLPEMQVGEWLLFEDMGAYTVVGTSSFNGFQSPTIYYVVSGLPDHVVRELKSQKS

来源 Source

来源生物 organism	Trypanosoma brucei gambiense
NCBI 分类编号 ncbi_taxonomy_id	31285
宿主生物 host_organism	Escherichia coli BL21

Entity 2 non-polymer

描述 description	GENETICIN
分子量 formula_weight	496.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE
分子量 formula_weight	363.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	207

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1njja1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
家族 Family family	b.49.2.3 — Eukaryotic ODC-like

结构域编号 domain_id	d1njja2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.6 — PLP-binding barrel
家族 Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

结构域编号 domain_id	d1njjb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
家族 Family family	b.49.2.3 — Eukaryotic ODC-like

结构域编号 domain_id	d1njjb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.6 — PLP-binding barrel
家族 Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

结构域编号 domain_id	d1njjc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
家族 Family family	b.49.2.3 — Eukaryotic ODC-like

结构域编号 domain_id	d1njjc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.6 — PLP-binding barrel
家族 Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

结构域编号 domain_id	d1njjd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
家族 Family family	b.49.2.3 — Eukaryotic ODC-like

结构域编号 domain_id	d1njjd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.6 — PLP-binding barrel
家族 Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1njjA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

结构域编号 domain_id	1njjA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	10 — Alanine racemase

结构域编号 domain_id	1njjB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

结构域编号 domain_id	1njjB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	10 — Alanine racemase

结构域编号 domain_id	1njjC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

结构域编号 domain_id	1njjC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	10 — Alanine racemase

结构域编号 domain_id	1njjD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

结构域编号 domain_id	1njjD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	10 — Alanine racemase

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	67.818 Å
晶胞边长 b length_b	88.540 Å
晶胞边长 c length_c	150.445 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.03 °
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	2.450 Å
最低分辨率 resolution_low	35.000 Å
R 因子 r_factor	—
R_work r_work	0.2600
R_free r_free	0.2830

fit	/app/data/saxs_computation/nj/1njj/1njj.fit
pddf	/app/data/pr_computation/nj/1njj/1njj.pr.out
profile	/app/data/saxs_computation/nj/1njj/1njj.dat