SAXSdb — 2gox

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gox
沉积日期 deposition_date	2006-04-14
结构标题 title	Crystal structure of Efb-C / C3d Complex
关键词 keywords	PROTEIN-PROTEIN COMPLEX, CELL ADHESION-TOXIN COMPLEX; CELL ADHESION/TOXIN
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	28.81 Å
回转半径 Rg (电子) rg_electron	27.98 Å
零角强度 I(0) i0	99913800.00
分子量 molecular_weight	80502.0 kDa
排除体积 excluded_volume	101700 Å³
包络体积 envelope_volume	120880 Å³
水化壳体积 shell_volume	35753 Å³
包络直径 envelope_diameter	100.1 Å
壳层 Rg shell_rg	35.39 Å
包络 Rg envelope_rg	28.07 Å
形状 Rg shape_rg	27.93 Å
总 Rg total_rg	28.87 Å
总原子数 total_atoms	5674
残基数 n_residues	724
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	93.6 Å
Rg (实空间) rg_real	28.76 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	9.9910e+07
I(0) 误差 (实空间) i0_real_error	1.2670e+06
Rg (倒空间) rg_reciprocal	28.79 Å
I(0) (倒空间) i0_reciprocal	99920000.0000
解质量估计 total_estimate	0.6804
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	34.0 Å
偏度 Skewness skewness	0.290
峰度 Kurtosis kurtosis	-0.451
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21870000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.992; Smooth: 0.979

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Complement C3
分子量 formula_weight	33143.9 kDa
突变 mutation	C1010A
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,C
原子数 atom_count	5991

GSRSTDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	Fibrinogen-binding protein
分子量 formula_weight	7592.9 kDa
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	B,D

TDATIKKEQKLIQAQNLVREFEKTHTVSAHRKAQKAVNLVSFEYKVKKMVLQERIDNVLKQGLVR

来源 Source

来源生物 organism	Staphylococcus aureus subsp. aureus Mu50
NCBI 分类编号 ncbi_taxonomy_id	158878
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	317

▼

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d2goxa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
家族 Family family	a.102.4.4 — Complement components

结构域编号 domain_id	d2goxa2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2goxb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.7 — Spectrin repeat-like
超家族 Superfamily superfamily	a.7.17 — Efb C-domain-like
家族 Family family	a.7.17.1 — Efb C-domain-like

结构域编号 domain_id	d2goxc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
家族 Family family	a.102.4.4 — Complement components

结构域编号 domain_id	d2goxc2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2goxd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.7 — Spectrin repeat-like
超家族 Superfamily superfamily	a.7.17 — Efb C-domain-like
家族 Family family	a.7.17.1 — Efb C-domain-like

CATH v4.4 (4 domains)

结构域编号 domain_id	2goxA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2goxB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	1270 — Sbi, C3 binding domain IV

结构域编号 domain_id	2goxC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2goxD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	1270 — Sbi, C3 binding domain IV

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	90.939 Å
晶胞边长 b length_b	90.939 Å
晶胞边长 c length_c	122.242 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 41
空间群编号 int_tables_number	76
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.1810
R_free r_free	0.2310

fit	/app/data/saxs_computation/go/2gox/2gox.fit
pddf	/app/data/pr_computation/go/2gox/2gox.pr.out
profile	/app/data/saxs_computation/go/2gox/2gox.dat

Crystal structure of Efb-C / C3d 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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)