1uzj

Integrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-1, holo form.

Method: X-RAY DIFFRACTION D_max: 131.6 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1uzj
沉积日期 deposition_date	2004-03-12
结构标题 title	Integrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-1, holo form.
关键词 keywords	MATRIX PROTEIN, EXTRA-CELLULAR MATRIX, FIBRILLIN-1, CBEGF DOMAIN, TB DOMAIN MATRIX PROTEIN; MATRIX PROTEIN
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	35.76 Å
回转半径 Rg (电子) rg_electron	36.39 Å
零角强度 I(0) i0	52688000.00
分子量 molecular_weight	52121.0 kDa
排除体积 excluded_volume	62953 Å³
包络体积 envelope_volume	95526 Å³
水化壳体积 shell_volume	25685 Å³
包络直径 envelope_diameter	138.4 Å
壳层 Rg shell_rg	36.08 Å
包络 Rg envelope_rg	35.79 Å
形状 Rg shape_rg	36.37 Å
总 Rg total_rg	36.41 Å
总原子数 total_atoms	3591
残基数 n_residues	486
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	131.6 Å
Rg (实空间) rg_real	36.29 Å
Rg 误差 (实空间) rg_real_error	1.52 Å
I(0) (实空间) i0_real	5.2690e+07
I(0) 误差 (实空间) i0_real_error	1.0040e+06
Rg (倒空间) rg_reciprocal	35.96 Å
I(0) (倒空间) i0_reciprocal	52670000.0000
解质量估计 total_estimate	0.7753
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	26.9 Å
偏度 Skewness skewness	0.573
峰度 Kurtosis kurtosis	-0.293
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	2378000.0000
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: 0.623; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.332; Smooth: 0.872

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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	FIBRILLIN-1
分子量 formula_weight	17332.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	3806

TDVNECLDPTTCISGNCVNTPGSYICDCPPDFELNPTRVGCVDTRSGNCYLDIRPRGDNGDTACSNEIGVGVSKASCCCSLGKAWGTPCEMCPAVNTSEYKILCPGGEGFRPNPITVILEDIDECQELPGLCQGGKCINTFGSFQCRCPTGYYLNEDTRVCD

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

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 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	215

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1uzja1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1uzja2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1uzja3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.23 — TB module/8-cys domain
超家族 Superfamily superfamily	g.23.1 — TB module/8-cys domain
家族 Family family	g.23.1.1 — TB module/8-cys domain

结构域编号 domain_id	d1uzjb1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1uzjb2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1uzjb3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.23 — TB module/8-cys domain
超家族 Superfamily superfamily	g.23.1 — TB module/8-cys domain
家族 Family family	g.23.1.1 — TB module/8-cys domain

结构域编号 domain_id	d1uzjc1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1uzjc2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.1 — EGF-type module

结构域编号 domain_id	d1uzjc3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.23 — TB module/8-cys domain
超家族 Superfamily superfamily	g.23.1 — TB module/8-cys domain
家族 Family family	g.23.1.1 — TB module/8-cys domain

CATH v4.4 (9 domains)

结构域编号 domain_id	1uzjA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1uzjA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	290 — Extracellular Matrix Fibrillin
同源超家族 H-superfamily homologous superfamily	10 — TGF-beta binding (TB) domain

结构域编号 domain_id	1uzjA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1uzjB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1uzjB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	290 — Extracellular Matrix Fibrillin
同源超家族 H-superfamily homologous superfamily	10 — TGF-beta binding (TB) domain

结构域编号 domain_id	1uzjB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1uzjC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1uzjC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	290 — Extracellular Matrix Fibrillin
同源超家族 H-superfamily homologous superfamily	10 — TGF-beta binding (TB) domain

结构域编号 domain_id	1uzjC03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

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7. 引用文献 (1)

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晶胞边长 a length_a	43.100 Å
晶胞边长 b length_b	105.600 Å
晶胞边长 c length_c	65.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.20 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	6

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	30.000 Å
R 因子 r_factor	0.2470
R_work r_work	0.2470
R_free r_free	0.3180

fit	/app/data/saxs_computation/uz/1uzj/1uzj.fit
pddf	/app/data/pr_computation/uz/1uzj/1uzj.pr.out
profile	/app/data/saxs_computation/uz/1uzj/1uzj.dat