2fk3

;Structure of the Alzheimer's Amyloid Precursor Protein (APP) Copper Binding Domain in 'large unit cell' form ;

Method: X-RAY DIFFRACTION D_max: 82.3 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	2fk3
沉积日期 deposition_date	2006-01-04
结构标题 title	;Structure of the Alzheimer's Amyloid Precursor Protein (APP) Copper Binding Domain in 'large unit cell' form ;
关键词 keywords	Alpha-Beta Two-layered Sandwich, Non-Crystallographic Symmetry, METAL BINDING PROTEIN; METAL BINDING 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	25.91 Å
回转半径 Rg (电子) rg_electron	25.21 Å
零角强度 I(0) i0	59534800.00
分子量 molecular_weight	55630.0 kDa
排除体积 excluded_volume	67551 Å³
包络体积 envelope_volume	84021 Å³
水化壳体积 shell_volume	28501 Å³
包络直径 envelope_diameter	81.4 Å
壳层 Rg shell_rg	32.18 Å
包络 Rg envelope_rg	25.31 Å
形状 Rg shape_rg	25.17 Å
总 Rg total_rg	26.05 Å
总原子数 total_atoms	3801
残基数 n_residues	470
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	82.3 Å
Rg (实空间) rg_real	25.96 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	5.9530e+07
I(0) 误差 (实空间) i0_real_error	8.0220e+05
Rg (倒空间) rg_reciprocal	25.95 Å
I(0) (倒空间) i0_reciprocal	59530000.0000
解质量估计 total_estimate	0.8918
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	28.4 Å
偏度 Skewness skewness	0.413
峰度 Kurtosis kurtosis	-0.382
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7331000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.945

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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	Amyloid beta A4 protein precursor
分子量 formula_weight	6848.9 kDa
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	3990

EACKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPL

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	Pichia pastoris

Entity 2 non-polymer

描述 description	COPPER (II) ION
分子量 formula_weight	63.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	19

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	189

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

结构域编号 domain_id	d2fk3a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.3 — Amyloid beta a4 protein copper binding domain (domain 2)
家族 Family family	d.230.3.1 — Amyloid beta a4 protein copper binding domain (domain 2)

结构域编号 domain_id	d2fk3a2
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	d2fk3b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.3 — Amyloid beta a4 protein copper binding domain (domain 2)
家族 Family family	d.230.3.1 — Amyloid beta a4 protein copper binding domain (domain 2)

结构域编号 domain_id	d2fk3b2
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	d2fk3c1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.3 — Amyloid beta a4 protein copper binding domain (domain 2)
家族 Family family	d.230.3.1 — Amyloid beta a4 protein copper binding domain (domain 2)

结构域编号 domain_id	d2fk3c2
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	d2fk3d1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.3 — Amyloid beta a4 protein copper binding domain (domain 2)
家族 Family family	d.230.3.1 — Amyloid beta a4 protein copper binding domain (domain 2)

结构域编号 domain_id	d2fk3d2
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	d2fk3e1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.3 — Amyloid beta a4 protein copper binding domain (domain 2)
家族 Family family	d.230.3.1 — Amyloid beta a4 protein copper binding domain (domain 2)

结构域编号 domain_id	d2fk3e2
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	d2fk3f1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.3 — Amyloid beta a4 protein copper binding domain (domain 2)
家族 Family family	d.230.3.1 — Amyloid beta a4 protein copper binding domain (domain 2)

结构域编号 domain_id	d2fk3f2
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	d2fk3g1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.3 — Amyloid beta a4 protein copper binding domain (domain 2)
家族 Family family	d.230.3.1 — Amyloid beta a4 protein copper binding domain (domain 2)

结构域编号 domain_id	d2fk3g2
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	d2fk3h1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.3 — Amyloid beta a4 protein copper binding domain (domain 2)
家族 Family family	d.230.3.1 — Amyloid beta a4 protein copper binding domain (domain 2)

结构域编号 domain_id	d2fk3h2
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	2fk3A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

结构域编号 domain_id	2fk3B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

结构域编号 domain_id	2fk3C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

结构域编号 domain_id	2fk3D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

结构域编号 domain_id	2fk3E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

结构域编号 domain_id	2fk3F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

结构域编号 domain_id	2fk3G00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

结构域编号 domain_id	2fk3H00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

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7. 引用文献 (1)

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晶胞边长 a length_a	59.623 Å
晶胞边长 b length_b	67.437 Å
晶胞边长 c length_c	127.656 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	32

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	19.880 Å
R 因子 r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2480

fit	/app/data/saxs_computation/fk/2fk3/2fk3.fit
pddf	/app/data/pr_computation/fk/2fk3/2fk3.pr.out
profile	/app/data/saxs_computation/fk/2fk3/2fk3.dat

;Structure of the Alzheimer's Amyloid Precursor Protein (APP) Copper Binding Domain in 'large unit cell' form ;

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) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)