SAXSdb — 1l6g

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1l6g
沉积日期 deposition_date	2002-03-10
结构标题 title	;Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine ;
关键词 keywords	;alanine racemase, reaction mechanism, N-(5'-phosphopyridoxyl)-alanine, ISOMERASE ;; ISOMERASE
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	28.26 Å
回转半径 Rg (电子) rg_electron	27.41 Å
零角强度 I(0) i0	117035000.00
分子量 molecular_weight	86578.0 kDa
排除体积 excluded_volume	108820 Å³
包络体积 envelope_volume	124790 Å³
水化壳体积 shell_volume	37293 Å³
包络直径 envelope_diameter	92.4 Å
壳层 Rg shell_rg	35.47 Å
包络 Rg envelope_rg	27.49 Å
形状 Rg shape_rg	27.44 Å
总 Rg total_rg	28.07 Å
总原子数 total_atoms	6108
残基数 n_residues	762
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	89.2 Å
Rg (实空间) rg_real	28.22 Å
Rg 误差 (实空间) rg_real_error	0.48 Å
I(0) (实空间) i0_real	1.1700e+08
I(0) 误差 (实空间) i0_real_error	1.8770e+06
Rg (倒空间) rg_reciprocal	28.23 Å
I(0) (倒空间) i0_reciprocal	117000000.0000
解质量估计 total_estimate	0.8923
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	31.8 Å
偏度 Skewness skewness	0.353
峰度 Kurtosis kurtosis	-0.355
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	59260000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.886

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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 (3)

Entity 1 polymer

描述 description	alanine racemase
分子量 formula_weight	43695.1 kDa
EC 编号 ec_number	5.1.1.1
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	6355

MNDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIGRGESSA

来源 Source

来源生物 organism	Geobacillus stearothermophilus
NCBI 分类编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE
分子量 formula_weight	320.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	247

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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	d1l6ga1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
家族 Family family	b.49.2.2 — Alanine racemase-like, C-terminal domain

结构域编号 domain_id	d1l6ga2
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.1.6 — PLP-binding barrel
家族 Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

结构域编号 domain_id	d1l6gb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
超家族 Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
家族 Family family	b.49.2.2 — Alanine racemase-like, C-terminal domain

结构域编号 domain_id	d1l6gb2
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.1.6 — PLP-binding barrel
家族 Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1l6gA01
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	10 — Alanine racemase

结构域编号 domain_id	1l6gA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

结构域编号 domain_id	1l6gB01
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	10 — Alanine racemase

结构域编号 domain_id	1l6gB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

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7. 引用文献 (4)

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晶胞边长 a length_a	99.787 Å
晶胞边长 b length_b	90.714 Å
晶胞边长 c length_c	85.270 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	8

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	2.000 Å
最低分辨率 resolution_low	7.990 Å
R 因子 r_factor	0.1690
R_work r_work	0.1690
R_free r_free	0.2160

fit	/app/data/saxs_computation/l6/1l6g/1l6g.fit
pddf	/app/data/pr_computation/l6/1l6g/1l6g.pr.out
profile	/app/data/saxs_computation/l6/1l6g/1l6g.dat

;Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine ;

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