SAXSdb — 1r44

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r44
沉积日期 deposition_date	2003-10-03
结构标题 title	Crystal Structure of VanX
关键词 keywords	VanX, E.faecium, dipeptidase, HYDROLASE; HYDROLASE
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	49.34 Å
回转半径 Rg (电子) rg_electron	51.22 Å
零角强度 I(0) i0	303923000.00
分子量 molecular_weight	140640.0 kDa
排除体积 excluded_volume	174300 Å³
包络体积 envelope_volume	228470 Å³
水化壳体积 shell_volume	44042 Å³
包络直径 envelope_diameter	182.4 Å
壳层 Rg shell_rg	43.36 Å
包络 Rg envelope_rg	51.60 Å
形状 Rg shape_rg	51.22 Å
总 Rg total_rg	50.91 Å
总原子数 total_atoms	9912
残基数 n_residues	1212
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	171.4 Å
Rg (实空间) rg_real	50.83 Å
Rg 误差 (实空间) rg_real_error	2.37 Å
I(0) (实空间) i0_real	3.0390e+08
I(0) 误差 (实空间) i0_real_error	6.1520e+06
Rg (倒空间) rg_reciprocal	49.35 Å
I(0) (倒空间) i0_reciprocal	303300000.0000
解质量估计 total_estimate	0.6216
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.1 Å
偏度 Skewness skewness	0.689
峰度 Kurtosis kurtosis	-0.357
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	27710000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.282; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.157; Smooth: 0.077

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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	D-alanyl-D-alanine dipeptidase
分子量 formula_weight	23408.2 kDa
EC 编号 ec_number	3.4.13.-
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	9924

MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK

来源 Source

来源生物 organism	Enterococcus faecium
NCBI 分类编号 ncbi_taxonomy_id	1352
宿主生物 host_organism	Escherichia coli str. K12 substr. W3110

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	12

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1r44a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.65 — Hedgehog/DD-peptidase
超家族 Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
家族 Family family	d.65.1.4 — VanX-like

结构域编号 domain_id	d1r44b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.65 — Hedgehog/DD-peptidase
超家族 Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
家族 Family family	d.65.1.4 — VanX-like

结构域编号 domain_id	d1r44c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.65 — Hedgehog/DD-peptidase
超家族 Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
家族 Family family	d.65.1.4 — VanX-like

结构域编号 domain_id	d1r44d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.65 — Hedgehog/DD-peptidase
超家族 Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
家族 Family family	d.65.1.4 — VanX-like

结构域编号 domain_id	d1r44e_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.65 — Hedgehog/DD-peptidase
超家族 Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
家族 Family family	d.65.1.4 — VanX-like

结构域编号 domain_id	d1r44f_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.65 — Hedgehog/DD-peptidase
超家族 Superfamily superfamily	d.65.1 — Hedgehog/DD-peptidase
家族 Family family	d.65.1.4 — VanX-like

CATH v4.4 (6 domains)

结构域编号 domain_id	1r44A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1r44B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1r44C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1r44D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1r44E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1r44F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	82.597 Å
晶胞边长 b length_b	44.694 Å
晶胞边长 c length_c	169.428 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.76 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2580
R_work r_work	0.2540
R_free r_free	0.3010

fit	/app/data/saxs_computation/r4/1r44/1r44.fit
pddf	/app/data/pr_computation/r4/1r44/1r44.pr.out
profile	/app/data/saxs_computation/r4/1r44/1r44.dat

Crystal Structure of VanX

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