1ord

CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION D_max: 106.3 Å Quality: EXCELLENT

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	1ord
沉积日期 deposition_date	1995-02-08
结构标题 title	CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION
关键词 keywords	CARBOXY-LYASE; CARBOXY-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	34.61 Å
回转半径 Rg (电子) rg_electron	33.70 Å
零角强度 I(0) i0	413666000.00
分子量 molecular_weight	165520.0 kDa
排除体积 excluded_volume	206990 Å³
包络体积 envelope_volume	246870 Å³
水化壳体积 shell_volume	58155 Å³
包络直径 envelope_diameter	110.4 Å
壳层 Rg shell_rg	42.61 Å
包络 Rg envelope_rg	34.05 Å
形状 Rg shape_rg	33.69 Å
总 Rg total_rg	34.34 Å
总原子数 total_atoms	14240
残基数 n_residues	1460
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	106.3 Å
Rg (实空间) rg_real	34.44 Å
Rg 误差 (实空间) rg_real_error	0.63 Å
I(0) (实空间) i0_real	4.1370e+08
I(0) 误差 (实空间) i0_real_error	6.8670e+06
Rg (倒空间) rg_reciprocal	34.55 Å
I(0) (倒空间) i0_reciprocal	413700000.0000
解质量估计 total_estimate	0.9023
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	43.9 Å
偏度 Skewness skewness	0.148
峰度 Kurtosis kurtosis	-0.534
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	106800000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.924

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	ORNITHINE DECARBOXYLASE
分子量 formula_weight	82649.6 kDa
EC 编号 ec_number	4.1.1.17
来源方法 src_method	nat
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	14561

SSSLKIASTQEARQYFDTDRVVVDAVGSDFTDVGAVIAMDYETDVIDAADATKFGIPVFAVTKDAQAISADELKKIFHIIDLENKFDATVNAREIETAVNNYEDSILPPFFKSLKEYVSRGLIQFDCPGHQGGQYYRKHPAGREFYDFFGETVFRADLCNADVALGDLLIHEGPAVAAEKHAARVYNADKTYFVLGGSSNANNTVTSALVSNGDLVLFDRNNHKSVYNSALAMAGGRPVYLQTNRNPYGFIGGIYDSDFDEKKIRELAAKVDPERAKWKRPFRLAVIQLGTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIPMMRNSSPLLIDDLGPEDPGIIVVQSVHKQQAGFSQTSQIHKKDSHIKGQLRYCDHKHFNNSFNLFMSTSPFYPMYAALDVNAAMQEGEAGRKLWHDLLITTIEARKKLIKAGSMFRPFVPPVVNGKKWEDGDTEDMANNIDYWRFEKGAKWHAYEGYGDNQYYVDPNKFMLTTPGINPETGDYEDFGVPATIVANYLRDHGIIPEKSDLNSILFLMTPAETPAKMNNLITQLLQLQRLIEEDAPLKQVLPSIYAANEERYNGYTIRELCQELHDFYKNNNTFTYQKRLFLREFFPEQGMLPYEARQEFIRNHNKLVPLNKIEGEIALEGALPYPPGVFCVAPGEKWSETAVKYFTILQDGINNFPGFAPEIQGVYFKQEGDKVVAYGEVYDAEVAKNDDRYNN

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	107

▼

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1orda1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.1 — CheY-like
家族 Family family	c.23.1.4 — Ornithine decarboxylase N-terminal 'wing' domain

结构域编号 domain_id	d1orda2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.5 — Ornithine decarboxylase major domain

结构域编号 domain_id	d1orda3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.125 — Ornithine decarboxylase C-terminal domain
超家族 Superfamily superfamily	d.125.1 — Ornithine decarboxylase C-terminal domain
家族 Family family	d.125.1.1 — Ornithine decarboxylase C-terminal domain

结构域编号 domain_id	d1ordb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.1 — CheY-like
家族 Family family	c.23.1.4 — Ornithine decarboxylase N-terminal 'wing' domain

结构域编号 domain_id	d1ordb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.67 — PLP-dependent transferase-like
超家族 Superfamily superfamily	c.67.1 — PLP-dependent transferases
家族 Family family	c.67.1.5 — Ornithine decarboxylase major domain

结构域编号 domain_id	d1ordb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.125 — Ornithine decarboxylase C-terminal domain
超家族 Superfamily superfamily	d.125.1 — Ornithine decarboxylase C-terminal domain
家族 Family family	d.125.1.1 — Ornithine decarboxylase C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1ordA01
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	220 —

结构域编号 domain_id	1ordA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1ordA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1ordA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	100 — Ornithine Decarboxylase; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Orn/Lys/Arg decarboxylase, C-terminal domain

结构域编号 domain_id	1ordB01
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	220 —

结构域编号 domain_id	1ordB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	640 — Aspartate Aminotransferase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

结构域编号 domain_id	1ordB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1150 — Aspartate Aminotransferase, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

结构域编号 domain_id	1ordB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	100 — Ornithine Decarboxylase; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Orn/Lys/Arg decarboxylase, C-terminal domain

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	195.600 Å
晶胞边长 b length_b	195.600 Å
晶胞边长 c length_c	97.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 6
空间群编号 int_tables_number	168
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2680

fit	/app/data/saxs_computation/or/1ord/1ord.fit
pddf	/app/data/pr_computation/or/1ord/1ord.pr.out
profile	/app/data/saxs_computation/or/1ord/1ord.dat