2c2v

Crystal structure of the CHIP-UBC13-UEV1a complex

Method: X-RAY DIFFRACTION D_max: 225.8 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	2c2v
沉积日期 deposition_date	2005-09-30
结构标题 title	Crystal structure of the CHIP-UBC13-UEV1a complex
关键词 keywords	CHAPERONE, HEAT-SHOCK PROTEIN COMPLEX, E3 LIGASE, UBIQUITINYLATION, TPR, HEAT-SHOCK PROTEIN; CHAPERONE
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	70.64 Å
回转半径 Rg (电子) rg_electron	72.13 Å
零角强度 I(0) i0	388140000.00
分子量 molecular_weight	164980.0 kDa
排除体积 excluded_volume	207290 Å³
包络体积 envelope_volume	366950 Å³
水化壳体积 shell_volume	51836 Å³
包络直径 envelope_diameter	250.2 Å
壳层 Rg shell_rg	49.74 Å
包络 Rg envelope_rg	73.27 Å
形状 Rg shape_rg	72.10 Å
总 Rg total_rg	71.50 Å
总原子数 total_atoms	11601
残基数 n_residues	1458
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	225.8 Å
Rg (实空间) rg_real	71.27 Å
Rg 误差 (实空间) rg_real_error	2.24 Å
I(0) (实空间) i0_real	3.8750e+08
I(0) 误差 (实空间) i0_real_error	8.3980e+06
Rg (倒空间) rg_reciprocal	67.10 Å
I(0) (倒空间) i0_reciprocal	384900000.0000
解质量估计 total_estimate	0.7311
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	41.1 Å
偏度 Skewness skewness	0.601
峰度 Kurtosis kurtosis	-0.445
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0055
最高正则化参数 α highest_alpha	11810000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.344; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.569; Smooth: 0.906

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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 (4)

Entity 1 polymer

描述 description	Ubiquitin-conjugating enzyme E2 N
分子量 formula_weight	17241.8 kDa
EC 编号 ec_number	2.3.2.23
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	B,E,H,K
原子数 atom_count	11636

AGSAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

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 polymer

描述 description	Ubiquitin-conjugating enzyme E2 variant 1
分子量 formula_weight	16095.5 kDa
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	C,F,I,L

TTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMILGPPRTIYENRIYSLKIECGPKYPEAPPFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQCYSN

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 3 polymer

描述 description	STIP1 homology and U box-containing protein 1
分子量 formula_weight	9033.2 kDa
EC 编号 ec_number	2.3.2.27
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	S,T,U,V

DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDAFISENGWVEDY

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 4 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	35

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6. 折叠分类 (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d2c2vb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.20 — UBC-like
超家族 Superfamily superfamily	d.20.1 — UBC-like
家族 Family family	d.20.1.1 — UBC-related

结构域编号 domain_id	d2c2vb3
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	d2c2vc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.20 — UBC-like
超家族 Superfamily superfamily	d.20.1 — UBC-like
家族 Family family	d.20.1.1 — UBC-related

结构域编号 domain_id	d2c2ve_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.20 — UBC-like
超家族 Superfamily superfamily	d.20.1 — UBC-like
家族 Family family	d.20.1.1 — UBC-related

结构域编号 domain_id	d2c2vf_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.20 — UBC-like
超家族 Superfamily superfamily	d.20.1 — UBC-like
家族 Family family	d.20.1.1 — UBC-related

结构域编号 domain_id	d2c2vh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.20 — UBC-like
超家族 Superfamily superfamily	d.20.1 — UBC-like
家族 Family family	d.20.1.1 — UBC-related

结构域编号 domain_id	d2c2vi_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.20 — UBC-like
超家族 Superfamily superfamily	d.20.1 — UBC-like
家族 Family family	d.20.1.1 — UBC-related

结构域编号 domain_id	d2c2vk2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.20 — UBC-like
超家族 Superfamily superfamily	d.20.1 — UBC-like
家族 Family family	d.20.1.1 — UBC-related

结构域编号 domain_id	d2c2vk3
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	d2c2vl_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.20 — UBC-like
超家族 Superfamily superfamily	d.20.1 — UBC-like
家族 Family family	d.20.1.1 — UBC-related

结构域编号 domain_id	d2c2vs1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.44 — RING/U-box
超家族 Superfamily superfamily	g.44.1 — RING/U-box
家族 Family family	g.44.1.2 — U-box

结构域编号 domain_id	d2c2vt_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.44 — RING/U-box
超家族 Superfamily superfamily	g.44.1 — RING/U-box
家族 Family family	g.44.1.0 — automated matches

结构域编号 domain_id	d2c2vu_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.44 — RING/U-box
超家族 Superfamily superfamily	g.44.1 — RING/U-box
家族 Family family	g.44.1.0 — automated matches

结构域编号 domain_id	d2c2vv_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.44 — RING/U-box
超家族 Superfamily superfamily	g.44.1 — RING/U-box
家族 Family family	g.44.1.0 — automated matches

CATH v4.4 (12 domains)

结构域编号 domain_id	2c2vB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	110 — Ubiquitin Conjugating Enzyme
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

结构域编号 domain_id	2c2vC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	110 — Ubiquitin Conjugating Enzyme
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

结构域编号 domain_id	2c2vE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	110 — Ubiquitin Conjugating Enzyme
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

结构域编号 domain_id	2c2vF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	110 — Ubiquitin Conjugating Enzyme
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

结构域编号 domain_id	2c2vH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	110 — Ubiquitin Conjugating Enzyme
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

结构域编号 domain_id	2c2vI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	110 — Ubiquitin Conjugating Enzyme
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

结构域编号 domain_id	2c2vK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	110 — Ubiquitin Conjugating Enzyme
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

结构域编号 domain_id	2c2vL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	110 — Ubiquitin Conjugating Enzyme
同源超家族 H-superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

结构域编号 domain_id	2c2vS00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	40 — Herpes Virus-1
同源超家族 H-superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

结构域编号 domain_id	2c2vT00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	40 — Herpes Virus-1
同源超家族 H-superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

结构域编号 domain_id	2c2vU00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	40 — Herpes Virus-1
同源超家族 H-superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

结构域编号 domain_id	2c2vV00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	40 — Herpes Virus-1
同源超家族 H-superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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7. 引用文献 (1)

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晶胞边长 a length_a	180.310 Å
晶胞边长 b length_b	69.991 Å
晶胞边长 c length_c	204.477 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.95 °
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	2.900 Å
最低分辨率 resolution_low	196.120 Å
R 因子 r_factor	0.2180
R_work r_work	0.2140
R_free r_free	0.2970

fit	/app/data/saxs_computation/c2/2c2v/2c2v.fit
pddf	/app/data/pr_computation/c2/2c2v/2c2v.pr.out
profile	/app/data/saxs_computation/c2/2c2v/2c2v.dat

Crystal structure of the CHIP-UBC13-UEV1a 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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 water

6. 折叠分类 (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)