1m5w

;1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate ;

Method: X-RAY DIFFRACTION D_max: 112.8 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	1m5w
沉积日期 deposition_date	2002-07-10
结构标题 title	;1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate ;
关键词 keywords	TIM barrel, protein-substrate complex, multi-binding states, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	37.24 Å
回转半径 Rg (电子) rg_electron	36.27 Å
零角强度 I(0) i0	722736000.00
分子量 molecular_weight	211440.0 kDa
排除体积 excluded_volume	261940 Å³
包络体积 envelope_volume	326930 Å³
水化壳体积 shell_volume	70859 Å³
包络直径 envelope_diameter	114.1 Å
壳层 Rg shell_rg	45.42 Å
包络 Rg envelope_rg	36.04 Å
形状 Rg shape_rg	36.25 Å
总 Rg total_rg	36.82 Å
总原子数 total_atoms	14784
残基数 n_residues	1936
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	112.8 Å
Rg (实空间) rg_real	36.93 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	7.2270e+08
I(0) 误差 (实空间) i0_real_error	1.0650e+07
Rg (倒空间) rg_reciprocal	37.13 Å
I(0) (倒空间) i0_reciprocal	722900000.0000
解质量估计 total_estimate	0.8891
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	51.0 Å
偏度 Skewness skewness	0.046
峰度 Kurtosis kurtosis	-0.469
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	390500000.0000
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: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.917

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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	Pyridoxal phosphate biosynthetic protein pdxJ
分子量 formula_weight	26421.3 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	15727

MAELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG

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 BL21(DE3)

Entity 2 non-polymer

描述 description	1-DEOXY-D-XYLULOSE-5-PHOSPHATE
分子量 formula_weight	214.1 kDa
来源方法 src_method	man
拷贝数 entity_count	6

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	2

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	943

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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	d1m5wa_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1m5wb_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1m5wc_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1m5wd_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1m5we_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1m5wf_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1m5wg_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

结构域编号 domain_id	d1m5wh_
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.1.24 — Pyridoxine 5'-phosphate synthase
家族 Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

CATH v4.4 (8 domains)

结构域编号 domain_id	1m5wA00
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	70 — Aldolase class I

结构域编号 domain_id	1m5wB00
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	70 — Aldolase class I

结构域编号 domain_id	1m5wC00
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	70 — Aldolase class I

结构域编号 domain_id	1m5wD00
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	70 — Aldolase class I

结构域编号 domain_id	1m5wE00
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	70 — Aldolase class I

结构域编号 domain_id	1m5wF00
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	70 — Aldolase class I

结构域编号 domain_id	1m5wG00
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	70 — Aldolase class I

结构域编号 domain_id	1m5wH00
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	70 — Aldolase class I

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7. 引用文献 (1)

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晶胞边长 a length_a	100.007 Å
晶胞边长 b length_b	129.404 Å
晶胞边长 c length_c	176.088 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	1.960 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.2360
R_work r_work	0.1950
R_free r_free	0.2490

fit	/app/data/saxs_computation/m5/1m5w/1m5w.fit
pddf	/app/data/pr_computation/m5/1m5w/1m5w.pr.out
profile	/app/data/saxs_computation/m5/1m5w/1m5w.dat