2hk9

Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution

Method: X-RAY DIFFRACTION D_max: 114.6 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	2hk9
沉积日期 deposition_date	2006-07-03
结构标题 title	Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution
关键词 keywords	shikimate pathway, shikimate dehydrogenase, drug design, oxidoreductase; OXIDOREDUCTASE
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	35.00 Å
回转半径 Rg (电子) rg_electron	34.53 Å
零角强度 I(0) i0	201520000.00
分子量 molecular_weight	122820.0 kDa
排除体积 excluded_volume	157380 Å³
包络体积 envelope_volume	192930 Å³
水化壳体积 shell_volume	46295 Å³
包络直径 envelope_diameter	115.1 Å
壳层 Rg shell_rg	41.30 Å
包络 Rg envelope_rg	34.29 Å
形状 Rg shape_rg	34.50 Å
总 Rg total_rg	35.14 Å
总原子数 total_atoms	8667
残基数 n_residues	1068
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	114.6 Å
Rg (实空间) rg_real	34.98 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	2.0150e+08
I(0) 误差 (实空间) i0_real_error	3.3860e+06
Rg (倒空间) rg_reciprocal	35.00 Å
I(0) (倒空间) i0_reciprocal	201500000.0000
解质量估计 total_estimate	0.8955
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	40.7 Å
偏度 Skewness skewness	0.290
峰度 Kurtosis kurtosis	-0.479
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	80460000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.904

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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	Shikimate dehydrogenase
分子量 formula_weight	30942.0 kDa
EC 编号 ec_number	1.1.1.25
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	8871

HHHHHHMINAQTQLYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKVKGINVTVPFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPEVKEKSILVLGAGGASRAVIYALVKEGAKVFLWNRTKEKAIKLAQKFPLEVVNSPEEVIDKVQVIVNTTSVGLKDEDPEIFNYDLIKKDHVVVDIIYKETKLLKKAKEKGAKLLDGLPMLLWQGIEAFKIWNGCEVPYSVAERSVRDLRG

来源 Source

来源生物 organism	Aquifex aeolicus
NCBI 分类编号 ncbi_taxonomy_id	63363
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID
分子量 formula_weight	174.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	743.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	204

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2hk9a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.5 — Shikimate dehydrogenase-like

结构域编号 domain_id	d2hk9a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d2hk9b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.5 — Shikimate dehydrogenase-like

结构域编号 domain_id	d2hk9b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d2hk9c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.5 — Shikimate dehydrogenase-like

结构域编号 domain_id	d2hk9c2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d2hk9d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family family	c.58.1.5 — Shikimate dehydrogenase-like

结构域编号 domain_id	d2hk9d2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	2hk9A01
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	10860 — Leucine Dehydrogenase, chain A, domain 1

结构域编号 domain_id	2hk9A02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2hk9B01
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	10860 — Leucine Dehydrogenase, chain A, domain 1

结构域编号 domain_id	2hk9B02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2hk9C01
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	10860 — Leucine Dehydrogenase, chain A, domain 1

结构域编号 domain_id	2hk9C02
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	2hk9D01
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	10860 — Leucine Dehydrogenase, chain A, domain 1

结构域编号 domain_id	2hk9D02
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	720 — NAD(P)-binding Rossmann-like Domain

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7. 引用文献 (1)

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晶胞边长 a length_a	71.999 Å
晶胞边长 b length_b	119.803 Å
晶胞边长 c length_c	128.872 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	16

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	2.200 Å
最低分辨率 resolution_low	29.410 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2710

fit	/app/data/saxs_computation/hk/2hk9/2hk9.fit
pddf	/app/data/pr_computation/hk/2hk9/2hk9.pr.out
profile	/app/data/saxs_computation/hk/2hk9/2hk9.dat