1z3u

Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition

Method: X-RAY DIFFRACTION D_max: 185.9 Å Quality: REASONABLE

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	1z3u
沉积日期 deposition_date	2005-03-14
结构标题 title	Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition
关键词 keywords	Tie2 binding, angiogenesis, extracellular ligand, SIGNALING PROTEIN; SIGNALING 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	61.86 Å
回转半径 Rg (电子) rg_electron	61.19 Å
零角强度 I(0) i0	143737000.00
分子量 molecular_weight	97781.0 kDa
排除体积 excluded_volume	120710 Å³
包络体积 envelope_volume	219390 Å³
水化壳体积 shell_volume	29774 Å³
包络直径 envelope_diameter	157.2 Å
壳层 Rg shell_rg	69.89 Å
包络 Rg envelope_rg	54.86 Å
形状 Rg shape_rg	61.19 Å
总 Rg total_rg	61.37 Å
总原子数 total_atoms	6880
残基数 n_residues	864
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	185.9 Å
Rg (实空间) rg_real	61.34 Å
Rg 误差 (实空间) rg_real_error	2.24 Å
I(0) (实空间) i0_real	1.4370e+08
I(0) 误差 (实空间) i0_real_error	3.1780e+06
Rg (倒空间) rg_reciprocal	62.23 Å
I(0) (倒空间) i0_reciprocal	143900000.0000
解质量估计 total_estimate	0.6084
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	4
主峰位置 r_peak_primary	104.1 Å
偏度 Skewness skewness	-0.601
峰度 Kurtosis kurtosis	-1.016
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2510000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.001; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.000

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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	Angiopoietin-2
分子量 formula_weight	24597.4 kDa
突变 mutation	F469A, Y475A, Y476A
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	7259

SFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKANGIKWAAWKGSGYSLKATTMMIRPADF

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	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	379

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1z3ua1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
家族 Family family	d.171.1.0 — automated matches

结构域编号 domain_id	d1z3ua2
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	d1z3ub1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
家族 Family family	d.171.1.0 — automated matches

结构域编号 domain_id	d1z3ub2
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	d1z3uc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
家族 Family family	d.171.1.0 — automated matches

结构域编号 domain_id	d1z3uc2
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	d1z3ud1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamily	d.171.1 — Fibrinogen C-terminal domain-like
家族 Family family	d.171.1.0 — automated matches

结构域编号 domain_id	d1z3ud2
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

CATH v4.4 (8 domains)

结构域编号 domain_id	1z3uA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	1z3uA02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	1z3uB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	1z3uB02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	1z3uC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	1z3uC02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	1z3uD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	1z3uD02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	140.218 Å
晶胞边长 b length_b	94.468 Å
晶胞边长 c length_c	84.673 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.47 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	16

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	2.250 Å
最低分辨率 resolution_low	8.000 Å
R 因子 r_factor	0.2460
R_work r_work	0.2460
R_free r_free	0.2780

fit	/app/data/saxs_computation/z3/1z3u/1z3u.fit
pddf	/app/data/pr_computation/z3/1z3u/1z3u.pr.out
profile	/app/data/saxs_computation/z3/1z3u/1z3u.dat