1xi5

Clathrin D6 coat with auxilin J-domain

Method: ELECTRON MICROSCOPY D_max: 374.3 Å Quality: EXCELLENT

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	1xi5
沉积日期 deposition_date	2004-09-21
结构标题 title	Clathrin D6 coat with auxilin J-domain
关键词 keywords	clathrin, alpha-zig-zag, beta-propeller, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
实验方法 method	ELECTRON MICROSCOPY

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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	— Å
回转半径 Rg (电子) rg_electron	141.50 Å
零角强度 I(0) i0	43247900000.00
分子量 molecular_weight	1802700.0 kDa
排除体积 excluded_volume	2213300 Å³
包络体积 envelope_volume	4439900 Å³
水化壳体积 shell_volume	281680 Å³
包络直径 envelope_diameter	489.4 Å
壳层 Rg shell_rg	108.10 Å
包络 Rg envelope_rg	130.90 Å
形状 Rg shape_rg	141.40 Å
总 Rg total_rg	141.30 Å
总原子数 total_atoms	—
残基数 n_residues	—
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	374.3 Å
Rg (实空间) rg_real	134.90 Å
Rg 误差 (实空间) rg_real_error	1.67 Å
I(0) (实空间) i0_real	4.1440e+10
I(0) 误差 (实空间) i0_real_error	8.7980e+08
Rg (倒空间) rg_reciprocal	127.60 Å
I(0) (倒空间) i0_reciprocal	40750000000.0000
解质量估计 total_estimate	0.9130
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	136.1 Å
偏度 Skewness skewness	0.176
峰度 Kurtosis kurtosis	-0.780
角度范围 angular_range	— – 0.0550 Å⁻¹
当前正则化参数 α current_alpha	0.8376
最高正则化参数 α highest_alpha	2198000000.0000
实空间数据点数 n_real_points	12
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.005; Oscil: 0.992; Stabil: 0.978; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; 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 (2)

Entity 1 polymer

描述 description	Clathrin heavy chain
分子量 formula_weight	187145.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	9

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,I
原子数 atom_count	15696

MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGAEELFARKFNALFAQGNYSEAAKVAANAPKGILRTPDTIRRFQSVPAQPGQTSPLLQYFGILLDQGQLNKYESLELCRPVLQQGRKQLLEKWLKEDKLECSEELGDLVKSVDPTLALSVYLRANVPNKVIQCFAETGQVQKIVLYAKKVGYTPDWIFLLRNVMRISPDQGQQFAQMLVQDEEPLADITQIVDVFMEYNLIQQCTAFLLDALKNNRPSEGPLQTRLLEMNLMHAPQVADAILGNQMFTHYDRAHIAQLCEKAGLLQRALEHFTDLYDIKRAVVHTHLLNPEWLVNYFGSLSVEDSLECLRAMLSANIRQNLQICVQVASKYHEQLSTQSLIELFESFKSFEGLFYFLGSIVNFSQDPDVHFKYIQAACKTGQIKEVERICRESNCYDPERVKNFLKEAKLTDQLPLIIVCDRFDFVHDLVLYLYRNNLQKYIEIYVQKVNPSRLPVVIGGLLDVDCSEDVIKNLILVVRGQFSTDELVAEVEKRNRLKLLLPWLEARIHEGCEEPATHNALAKIYIDSNNNPERFLRENPYYDSRVVGKYCEKRDPHLACVAYERGQCDLELINVCNENSLFKSLSRYLVRRKDPELWGSVLLESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIANIAISNELFEEAFAIFRKFDVNTSAVQVLIEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEKHELIEFRRIAAYLFKGNNRWKQSVELCKKDSLYKDAMQYASESKDTELAEELLQWFLQEEKRECFGACLFTCYDLLRPDVVLETAWRHNIMDFAMPYFIQVMKEYLTKVDKLDASESLRKEEEQATETQ

Entity 2 polymer

描述 description	Auxilin J-domain
分子量 formula_weight	13383.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J,K,L,M,N,O,P,Q,R

PRTIAEMRKEEMAKEMDPEKLKILEWIEGKERNIRALLSTMHTVLWAGETKWKPVGMADLVTPEQVKKVYRKAVLVVHPDKATGQPYEQYAKMIFMELNDAWSEFENQGQKPLY

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (18 domains)

结构域编号 domain_id	d1xi5a_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5b_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5c_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5d_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5e_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5f_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5g_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5h_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5i_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5j_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5k_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5l_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5m_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5n_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5o_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5p_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5q_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

结构域编号 domain_id	d1xi5r_
类 Class class	i — Low resolution protein structures
折叠类型 Fold fold	i.23 — clathrin assemblies
超家族 Superfamily superfamily	i.23.1 — clathrin assemblies
家族 Family family	i.23.1.1 — clathrin assemblies

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7. 引用文献 (2)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	1

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

分辨率 resolution	12.00 Å
分辨率测定方法 resolution_method	FOURIER SPACE RECONSTRUCTION
颗粒数 num_particles	900

fit	/app/data/saxs_computation/xi/1xi5/1xi5.fit
pddf	/app/data/pr_computation/xi/1xi5/1xi5.pr.out
profile	/app/data/saxs_computation/xi/1xi5/1xi5.dat

Clathrin D6 coat with auxilin J-domain

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (18 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)