2bt4

Type II Dehydroquinase inhibitor complex

Method: X-RAY DIFFRACTION D_max: 104.1 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	2bt4
沉积日期 deposition_date	2005-05-26
结构标题 title	Type II Dehydroquinase inhibitor complex
关键词 keywords	SHIKIMATE PATHWAY, DEHYDROQUINATE, LYASE, AMINO-ACID BIOSYNTHESIS, AROMATIC AMINO ACID BIOSYNTHESIS; LYASE
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	35.90 Å
回转半径 Rg (电子) rg_electron	34.96 Å
零角强度 I(0) i0	628043000.00
分子量 molecular_weight	196700.0 kDa
排除体积 excluded_volume	243190 Å³
包络体积 envelope_volume	290540 Å³
水化壳体积 shell_volume	64990 Å³
包络直径 envelope_diameter	106.3 Å
壳层 Rg shell_rg	44.57 Å
包络 Rg envelope_rg	34.30 Å
形状 Rg shape_rg	34.92 Å
总 Rg total_rg	35.66 Å
总原子数 total_atoms	13840
残基数 n_residues	1788
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	104.1 Å
Rg (实空间) rg_real	35.57 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	6.2800e+08
I(0) 误差 (实空间) i0_real_error	9.6160e+06
Rg (倒空间) rg_reciprocal	35.77 Å
I(0) (倒空间) i0_reciprocal	628200000.0000
解质量估计 total_estimate	0.8935
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	49.7 Å
偏度 Skewness skewness	-0.064
峰度 Kurtosis kurtosis	-0.562
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	438100000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.889

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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 (6)

Entity 1 polymer

描述 description	3-DEHYDROQUINATE DEHYDRATASE
分子量 formula_weight	16700.8 kDa
EC 编号 ec_number	4.2.1.10
来源方法 src_method	man
拷贝数 entity_count	12

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,I,J,K,L
原子数 atom_count	15641

MPRSLANAPIMILNGPNLNLLGQRQPEIYGSDTLADVEALCVKAAAAHGGTVDFRQSNHEGELVDWIHEARLNHCGIVINPAAYSHTSVAILDALNTCDGLPVVEVHISNIHQREPFRHHSYVSQRADGVVAGCGVQGYVFGVERIAALAGAGSARA

来源 Source

来源生物 organism	STREPTOMYCES COELICOLOR
NCBI 分类编号 ncbi_taxonomy_id	1902
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	(1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID
分子量 formula_weight	310.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	12

Entity 6 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	1731

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2bt4a_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4b_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4c_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4d_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4e_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4f_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4g_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4h_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4i_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4j_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4k_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

结构域编号 domain_id	d2bt4l_
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.23.13 — Type II 3-dehydroquinate dehydratase
家族 Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

CATH v4.4 (12 domains)

结构域编号 domain_id	2bt4A00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4B00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4C00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4D00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4E00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4F00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4G00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4H00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4I00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4J00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4K00
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	9100 — Dehydroquinase, class II

结构域编号 domain_id	2bt4L00
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	9100 — Dehydroquinase, class II

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7. 引用文献 (2)

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晶胞边长 a length_a	196.616 Å
晶胞边长 b length_b	196.487 Å
晶胞边长 c length_c	240.626 Å
晶胞夹角 α angle_alpha	65.91 °
晶胞夹角 β angle_beta	65.91 °
晶胞夹角 γ angle_gamma	90.01 °
晶胞分子数 Z z_pdb	180

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	27.000 Å
R 因子 r_factor	0.1990
R_work r_work	0.1970
R_free r_free	0.2480

fit	/app/data/saxs_computation/bt/2bt4/2bt4.fit
pddf	/app/data/pr_computation/bt/2bt4/2bt4.pr.out
profile	/app/data/saxs_computation/bt/2bt4/2bt4.dat