1tkk

The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from Bacillus subtilis

Method: X-RAY DIFFRACTION D_max: 125.0 Å Quality: GOOD

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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1tkk
沉积日期 deposition_date	2004-06-08
结构标题 title	The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from Bacillus subtilis
关键词 keywords	epimerase, enolase super family, ISOMERASE; ISOMERASE
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	41.34 Å
回转半径 Rg (电子) rg_electron	40.88 Å
零角强度 I(0) i0	1379470000.00
分子量 molecular_weight	311310.0 kDa
排除体积 excluded_volume	391760 Å³
包络体积 envelope_volume	475640 Å³
水化壳体积 shell_volume	90530 Å³
包络直径 envelope_diameter	126.0 Å
壳层 Rg shell_rg	50.99 Å
包络 Rg envelope_rg	40.18 Å
形状 Rg shape_rg	40.86 Å
总 Rg total_rg	41.37 Å
总原子数 total_atoms	21740
残基数 n_residues	2864
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	125.0 Å
Rg (实空间) rg_real	41.06 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	1.3790e+09
I(0) 误差 (实空间) i0_real_error	2.2230e+07
Rg (倒空间) rg_reciprocal	41.34 Å
I(0) (倒空间) i0_reciprocal	1380000000.0000
解质量估计 total_estimate	0.8997
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	52.6 Å
偏度 Skewness skewness	0.039
峰度 Kurtosis kurtosis	-0.570
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	252100000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.959

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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	similar to chloromuconate cycloisomerase
分子量 formula_weight	39519.6 kDa
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,B,C,D,E,F,G,H
原子数 atom_count	23267

MKIIRIETSRIAVPLTKPFKTALRTVYTAESVIVRITYDSGAVGWGEAPPTLVITGDSMDSIESAIHHVLKPALLGKSLAGYEAILHDIQHLLTGNMSAKAAVEMALYDGWAQMCGLPLYQMLGGYRDTLETDYTVSVNSPEEMAADAENYLKQGFQTLKIKVGKDDIATDIARIQEIRKRVGSAVKLRLDANQGWRPKEAVTAIRKMEDAGLGIELVEQPVHKDDLAGLKKVTDATDTPIMADESVFTPRQAFEVLQTRSADLINIKLMKAGGISGAEKINAMAEACGVECMVGSMIETKLGITAAAHFAASKRNITRFDFDAPLMLKTDVFNGGITYSGSTISMPGKPGLGIIGAALLKGEKEQ

来源 Source

来源生物 organism	Bacillus subtilis
NCBI 分类编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 3 non-polymer

描述 description	ALANINE
分子量 formula_weight	89.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 4 non-polymer

描述 description	GLUTAMIC ACID
分子量 formula_weight	147.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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	1521

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6. 折叠分类 (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d1tkka1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d1tkka2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d1tkkb1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d1tkkb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d1tkkc1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d1tkkc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d1tkkd1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d1tkkd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d1tkke1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d1tkke2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d1tkkf1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d1tkkf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d1tkkg1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d1tkkg2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

结构域编号 domain_id	d1tkkh1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d1tkkh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.1 — Enolase N-terminal domain-like

CATH v4.4 (16 domains)

结构域编号 domain_id	1tkkA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1tkkA02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	1tkkB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1tkkB02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	1tkkC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1tkkC02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	1tkkD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1tkkD02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	1tkkE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1tkkE02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	1tkkF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1tkkF02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	1tkkG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1tkkG02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	1tkkH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	1tkkH02
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	120 — Enolase-like C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	117.400 Å
晶胞边长 b length_b	134.600 Å
晶胞边长 c length_c	194.900 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	90.00 °
晶胞分子数 Z z_pdb	32

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2220
R_work r_work	0.2190
R_free r_free	0.2850

fit	/app/data/saxs_computation/tk/1tkk/1tkk.fit
pddf	/app/data/pr_computation/tk/1tkk/1tkk.pr.out
profile	/app/data/saxs_computation/tk/1tkk/1tkk.dat