1k5h

1-deoxy-D-xylulose-5-phosphate reductoisomerase

Method: X-RAY DIFFRACTION D_max: 127.2 Å Quality: REASONABLE

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	1k5h
沉积日期 deposition_date	2001-10-10
结构标题 title	1-deoxy-D-xylulose-5-phosphate reductoisomerase
关键词 keywords	alpha-helix, beta-barrel, dinucleotide binding motif, variable loop, induced fit, 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	37.68 Å
回转半径 Rg (电子) rg_electron	37.39 Å
零角强度 I(0) i0	264597000.00
分子量 molecular_weight	129380.0 kDa
排除体积 excluded_volume	161130 Å³
包络体积 envelope_volume	210540 Å³
水化壳体积 shell_volume	47744 Å³
包络直径 envelope_diameter	134.4 Å
壳层 Rg shell_rg	42.79 Å
包络 Rg envelope_rg	37.02 Å
形状 Rg shape_rg	37.38 Å
总 Rg total_rg	37.77 Å
总原子数 total_atoms	9038
残基数 n_residues	1187
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	127.2 Å
Rg (实空间) rg_real	37.78 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	2.6460e+08
I(0) 误差 (实空间) i0_real_error	4.6450e+06
Rg (倒空间) rg_reciprocal	37.72 Å
I(0) (倒空间) i0_reciprocal	264600000.0000
解质量估计 total_estimate	0.6562
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	39.4 Å
偏度 Skewness skewness	0.377
峰度 Kurtosis kurtosis	-0.408
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31290000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 0.020; Positv: 1.000; Valcen: 0.983; Smooth: 0.878

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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 (2)

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1k5ha1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.69 — Left-handed superhelix
超家族 Superfamily superfamily	a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
家族 Family family	a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain

结构域编号 domain_id	d1k5ha2
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.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1k5ha3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

结构域编号 domain_id	d1k5hb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.69 — Left-handed superhelix
超家族 Superfamily superfamily	a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
家族 Family family	a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain

结构域编号 domain_id	d1k5hb2
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.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1k5hb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

结构域编号 domain_id	d1k5hc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.69 — Left-handed superhelix
超家族 Superfamily superfamily	a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
家族 Family family	a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain

结构域编号 domain_id	d1k5hc2
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.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1k5hc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

CATH v4.4 (6 domains)

结构域编号 domain_id	1k5hA01
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	1k5hA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

结构域编号 domain_id	1k5hB01
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	1k5hB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

结构域编号 domain_id	1k5hC01
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	1k5hC03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase sigma factor, region 2, helix turn helix motif

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7. 引用文献 (1)

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晶胞边长 a length_a	101.266 Å
晶胞边长 b length_b	249.263 Å
晶胞边长 c length_c	132.112 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	24

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	33.450 Å
R 因子 r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2840

描述 description	1-deoxy-D-xylulose-5-phosphate reductoisomerase
分子量 formula_weight	43431.9 kDa
EC 编号 ec_number	1.1.1.-
来源方法 src_method	man
拷贝数 entity_count	3

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	9126

1-deoxy-D-xylulose-5-phosphate reductoisomerase

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	88

fit	/app/data/saxs_computation/k5/1k5h/1k5h.fit
pddf	/app/data/pr_computation/k5/1k5h/1k5h.pr.out
profile	/app/data/saxs_computation/k5/1k5h/1k5h.dat