SAXSdb — 1gvm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gvm
沉积日期 deposition_date	2002-02-15
结构标题 title	CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE
关键词 keywords	CHOLINE-BINDING DOMAIN, CELL WALL ATTACHMENT; CHOLINE-BINDING DOMAIN
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	41.66 Å
回转半径 Rg (电子) rg_electron	42.03 Å
零角强度 I(0) i0	123611000.00
分子量 molecular_weight	92615.0 kDa
排除体积 excluded_volume	116820 Å³
包络体积 envelope_volume	176990 Å³
水化壳体积 shell_volume	39795 Å³
包络直径 envelope_diameter	160.3 Å
壳层 Rg shell_rg	41.05 Å
包络 Rg envelope_rg	41.59 Å
形状 Rg shape_rg	42.02 Å
总 Rg total_rg	41.99 Å
总原子数 total_atoms	6572
残基数 n_residues	769
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	153.2 Å
Rg (实空间) rg_real	42.20 Å
Rg 误差 (实空间) rg_real_error	2.27 Å
I(0) (实空间) i0_real	1.2360e+08
I(0) 误差 (实空间) i0_real_error	2.3200e+06
Rg (倒空间) rg_reciprocal	41.66 Å
I(0) (倒空间) i0_reciprocal	123500000.0000
解质量估计 total_estimate	0.7819
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	44.4 Å
偏度 Skewness skewness	0.716
峰度 Kurtosis kurtosis	0.138
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6089000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.529; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.846; Smooth: 0.726

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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 (5)

Entity 1 polymer

描述 description	AUTOLYSIN
分子量 formula_weight	15876.6 kDa
EC 编号 ec_number	3.5.1.28
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	6651

MKGGIVHSDGSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK

来源 Source

来源生物 organism	STREPTOCOCCUS PNEUMONIAE
通用名 common_name	PNEUMOCOCCUS
NCBI 分类编号 ncbi_taxonomy_id	1313
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	CHOLINE ION
分子量 formula_weight	104.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

Entity 3 non-polymer

描述 description	DECYLAMINE-N,N-DIMETHYL-N-OXIDE
分子量 formula_weight	201.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	79

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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	d1gvma_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.109 — beta-hairpin stack
超家族 Superfamily superfamily	b.109.1 — Cell wall binding repeat
家族 Family family	b.109.1.1 — Cell wall binding repeat

结构域编号 domain_id	d1gvmb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.109 — beta-hairpin stack
超家族 Superfamily superfamily	b.109.1 — Cell wall binding repeat
家族 Family family	b.109.1.1 — Cell wall binding repeat

结构域编号 domain_id	d1gvmc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.109 — beta-hairpin stack
超家族 Superfamily superfamily	b.109.1 — Cell wall binding repeat
家族 Family family	b.109.1.1 — Cell wall binding repeat

结构域编号 domain_id	d1gvmd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.109 — beta-hairpin stack
超家族 Superfamily superfamily	b.109.1 — Cell wall binding repeat
家族 Family family	b.109.1.1 — Cell wall binding repeat

结构域编号 domain_id	d1gvme_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.109 — beta-hairpin stack
超家族 Superfamily superfamily	b.109.1 — Cell wall binding repeat
家族 Family family	b.109.1.1 — Cell wall binding repeat

结构域编号 domain_id	d1gvmf_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.109 — beta-hairpin stack
超家族 Superfamily superfamily	b.109.1 — Cell wall binding repeat
家族 Family family	b.109.1.1 — Cell wall binding repeat

CATH v4.4 (6 domains)

结构域编号 domain_id	1gvmA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	270 — left handed beta-beta-3-solenoid
同源超家族 H-superfamily homologous superfamily	10 — Cholin Binding

结构域编号 domain_id	1gvmB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	270 — left handed beta-beta-3-solenoid
同源超家族 H-superfamily homologous superfamily	10 — Cholin Binding

结构域编号 domain_id	1gvmC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	270 — left handed beta-beta-3-solenoid
同源超家族 H-superfamily homologous superfamily	10 — Cholin Binding

结构域编号 domain_id	1gvmD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	270 — left handed beta-beta-3-solenoid
同源超家族 H-superfamily homologous superfamily	10 — Cholin Binding

结构域编号 domain_id	1gvmE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	270 — left handed beta-beta-3-solenoid
同源超家族 H-superfamily homologous superfamily	10 — Cholin Binding

结构域编号 domain_id	1gvmF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	270 — left handed beta-beta-3-solenoid
同源超家族 H-superfamily homologous superfamily	10 — Cholin Binding

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7. 引用文献 (2)

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晶胞边长 a length_a	56.717 Å
晶胞边长 b length_b	85.390 Å
晶胞边长 c length_c	204.136 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.54 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	8.000 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/gv/1gvm/1gvm.fit
pddf	/app/data/pr_computation/gv/1gvm/1gvm.pr.out
profile	/app/data/saxs_computation/gv/1gvm/1gvm.dat

CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)