SAXSdb — 1sa1

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1sa1
沉积日期 deposition_date	2004-02-06
结构标题 title	Tubulin-podophyllotoxin: stathmin-like domain complex
关键词 keywords	ALPHA-TUBULIN, BETA-TUBULIN, COLCHICINE, GTPASE, MICROTUBULE PODOPHYLLOTOXIN, STATHMIN, TUBULIN, CELL CYCLE; CELL CYCLE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	51.72 Å
回转半径 Rg (电子) rg_electron	52.56 Å
零角强度 I(0) i0	637826000.00
分子量 molecular_weight	201840.0 kDa
排除体积 excluded_volume	249060 Å³
包络体积 envelope_volume	330550 Å³
水化壳体积 shell_volume	58712 Å³
包络直径 envelope_diameter	185.6 Å
壳层 Rg shell_rg	46.83 Å
包络 Rg envelope_rg	52.84 Å
形状 Rg shape_rg	52.58 Å
总 Rg total_rg	52.32 Å
总原子数 total_atoms	14180
残基数 n_residues	1845
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	174.1 Å
Rg (实空间) rg_real	52.43 Å
Rg 误差 (实空间) rg_real_error	2.40 Å
I(0) (实空间) i0_real	6.3780e+08
I(0) 误差 (实空间) i0_real_error	1.3890e+07
Rg (倒空间) rg_reciprocal	51.12 Å
I(0) (倒空间) i0_reciprocal	636700000.0000
解质量估计 total_estimate	0.6921
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	34.8 Å
偏度 Skewness skewness	0.651
峰度 Kurtosis kurtosis	-0.404
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	111400000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.433; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.641; Smooth: 0.060

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (7)

Entity 1 polymer

描述 description	Tubulin alpha chain
分子量 formula_weight	50163.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	14180

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Entity 2 polymer

描述 description	Tubulin beta chain
分子量 formula_weight	49907.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEGEEDEA

Entity 3 polymer

描述 description	Stathmin 4
分子量 formula_weight	16713.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E

ADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKEEASR

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	GUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	GUANOSINE-5'-DIPHOSPHATE
分子量 formula_weight	443.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 non-polymer

描述 description	9-HYDROXY-5-(3,4,5-TRIMETHOXYPHENYL)-5,8,8A,9-TETRAHYDROFURO[3',4':6,7]NAPHTHO[2,3-D][1,3]DIOXOL-6(5AH)-ONE
分子量 formula_weight	414.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

▼

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1sa1a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.32 — Tubulin nucleotide-binding domain-like
超家族 Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
家族 Family family	c.32.1.1 — Tubulin, GTPase domain

结构域编号 domain_id	d1sa1a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
家族 Family family	d.79.2.1 — Tubulin, C-terminal domain

结构域编号 domain_id	d1sa1b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.32 — Tubulin nucleotide-binding domain-like
超家族 Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
家族 Family family	c.32.1.1 — Tubulin, GTPase domain

结构域编号 domain_id	d1sa1b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
家族 Family family	d.79.2.1 — Tubulin, C-terminal domain

结构域编号 domain_id	d1sa1c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.32 — Tubulin nucleotide-binding domain-like
超家族 Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
家族 Family family	c.32.1.1 — Tubulin, GTPase domain

结构域编号 domain_id	d1sa1c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
家族 Family family	d.79.2.1 — Tubulin, C-terminal domain

结构域编号 domain_id	d1sa1d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.32 — Tubulin nucleotide-binding domain-like
超家族 Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
家族 Family family	c.32.1.1 — Tubulin, GTPase domain

结构域编号 domain_id	d1sa1d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
家族 Family family	d.79.2.1 — Tubulin, C-terminal domain

结构域编号 domain_id	d1sa1e_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
超家族 Superfamily superfamily	a.137.10 — Stathmin
家族 Family family	a.137.10.1 — Stathmin

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	328.061 Å
晶胞边长 b length_b	328.061 Å
晶胞边长 c length_c	54.301 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	4.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2064
R_work r_work	0.2037
R_free r_free	0.2594

fit	/app/data/saxs_computation/sa/1sa1/1sa1.fit
pddf	/app/data/pr_computation/sa/1sa1/1sa1.pr.out
profile	/app/data/saxs_computation/sa/1sa1/1sa1.dat

Tubulin-podophyllotoxin: stathmin-like domain complex

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 (7)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)