SAXSdb — 1gml

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1gml
沉积日期 deposition_date	2001-09-17
结构标题 title	crystal structure of the mouse CCT gamma apical domain (triclinic)
关键词 keywords	CHAPERONE, CHAPERONIN, ACTIN, TUBULIN; CHAPERONE
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	35.61 Å
回转半径 Rg (电子) rg_electron	35.40 Å
零角强度 I(0) i0	77683300.00
分子量 molecular_weight	69184.0 kDa
排除体积 excluded_volume	86492 Å³
包络体积 envelope_volume	124810 Å³
水化壳体积 shell_volume	31776 Å³
包络直径 envelope_diameter	116.3 Å
壳层 Rg shell_rg	38.65 Å
包络 Rg envelope_rg	34.64 Å
形状 Rg shape_rg	35.40 Å
总 Rg total_rg	35.68 Å
总原子数 total_atoms	4839
残基数 n_residues	612
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	118.3 Å
Rg (实空间) rg_real	35.83 Å
Rg 误差 (实空间) rg_real_error	1.12 Å
I(0) (实空间) i0_real	7.7680e+07
I(0) 误差 (实空间) i0_real_error	1.4200e+06
Rg (倒空间) rg_reciprocal	35.70 Å
I(0) (倒空间) i0_reciprocal	77670000.0000
解质量估计 total_estimate	0.8492
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	43.0 Å
偏度 Skewness skewness	0.396
峰度 Kurtosis kurtosis	-0.568
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11390000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.748; Smooth: 0.760

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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	T-COMPLEX PROTEIN 1 SUBUNIT GAMMA
分子量 formula_weight	20644.7 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	5484

MEDSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEITREEDFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNRIARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGASHHHHHH

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	645

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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	d1gmla_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1gmlb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1gmlc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

结构域编号 domain_id	d1gmld_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
超家族 Superfamily superfamily	c.8.5 — GroEL apical domain-like
家族 Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1gmlA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1gmlB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1gmlC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

结构域编号 domain_id	1gmlD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	50 — 3-Layer(bba) Sandwich
拓扑 Topology topology	7 — GroEL
同源超家族 H-superfamily homologous superfamily	10 — GroEL

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7. 引用文献 (1)

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晶胞边长 a length_a	51.740 Å
晶胞边长 b length_b	65.020 Å
晶胞边长 c length_c	65.470 Å
晶胞夹角 α angle_alpha	89.97 °
晶胞夹角 β angle_beta	103.95 °
晶胞夹角 γ angle_gamma	90.35 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	28.950 Å
R 因子 r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2340

fit	/app/data/saxs_computation/gm/1gml/1gml.fit
pddf	/app/data/pr_computation/gm/1gml/1gml.pr.out
profile	/app/data/saxs_computation/gm/1gml/1gml.dat

crystal structure of the mouse CCT gamma apical domain (triclinic)

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)