SAXSdb — 1o9b

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1o9b
沉积日期 deposition_date	2002-12-12
结构标题 title	QUINATE/SHIKIMATE DEHYDROGENASE YDIB COMPLEXED WITH NADH
关键词 keywords	OXIDOREDUCTASE, QUINATE, SHIKIMATE, NAD, MONTREAL-KINGSTON BACTERIAL STRUCTURAL GENOMICS INITIATIVE, BSGI, STRUCTURAL GENOMICS; 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	31.18 Å
回转半径 Rg (电子) rg_electron	31.49 Å
零角强度 I(0) i0	69832400.00
分子量 molecular_weight	63650.0 kDa
排除体积 excluded_volume	78255 Å³
包络体积 envelope_volume	97362 Å³
水化壳体积 shell_volume	28323 Å³
包络直径 envelope_diameter	113.6 Å
壳层 Rg shell_rg	35.07 Å
包络 Rg envelope_rg	31.63 Å
形状 Rg shape_rg	31.57 Å
总 Rg total_rg	31.54 Å
总原子数 total_atoms	4387
残基数 n_residues	542
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	108.2 Å
Rg (实空间) rg_real	31.65 Å
Rg 误差 (实空间) rg_real_error	1.15 Å
I(0) (实空间) i0_real	6.9830e+07
I(0) 误差 (实空间) i0_real_error	1.0870e+06
Rg (倒空间) rg_reciprocal	31.45 Å
I(0) (倒空间) i0_reciprocal	69820000.0000
解质量估计 total_estimate	0.6751
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.5 Å
偏度 Skewness skewness	0.606
峰度 Kurtosis kurtosis	-0.401
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	57360000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.482; Stabil: 0.988; Sysdev: 1.000; Positv: 1.000; Valcen: 0.362; Smooth: 0.000

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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 (4)

Entity 1 polymer

描述 description	HYPOTHETICAL SHIKIMATE 5-DEHYDROGENASE-LIKE PROTEIN YDIB
分子量 formula_weight	31773.6 kDa
EC 编号 ec_number	1.1.1.25
来源方法 src_method	man
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	4541

MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
分子量 formula_weight	665.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	5

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	154

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1o9ba1
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	d1o9ba2
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	d1o9bb1
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	d1o9bb2
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

CATH v4.4 (4 domains)

结构域编号 domain_id	1o9bA01
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	1o9bA02
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	1o9bB01
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	1o9bB02
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	157.874 Å
晶胞边长 b length_b	157.874 Å
晶胞边长 c length_c	40.011 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 64
空间群编号 int_tables_number	172
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	19.800 Å
R 因子 r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2940

fit	/app/data/saxs_computation/o9/1o9b/1o9b.fit
pddf	/app/data/pr_computation/o9/1o9b/1o9b.pr.out
profile	/app/data/saxs_computation/o9/1o9b/1o9b.dat

QUINATE/SHIKIMATE DEHYDROGENASE YDIB COMPLEXED WITH NADH

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction