1gk4

HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2)

Method: X-RAY DIFFRACTION D_max: 108.2 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	1gk4
沉积日期 deposition_date	2001-08-08
结构标题 title	HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2)
关键词 keywords	VIMENTIN, INTERMEDIATE FILAMENT, DIMER, PARALLEL COILED COIL, HEPTAD REPEAT, STUTTER; VIMENTIN
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	41.58 Å
回转半径 Rg (电子) rg_electron	44.15 Å
零角强度 I(0) i0	50401000.00
分子量 molecular_weight	53263.0 kDa
排除体积 excluded_volume	65312 Å³
包络体积 envelope_volume	98810 Å³
水化壳体积 shell_volume	23716 Å³
包络直径 envelope_diameter	177.2 Å
壳层 Rg shell_rg	36.59 Å
包络 Rg envelope_rg	45.91 Å
形状 Rg shape_rg	44.14 Å
总 Rg total_rg	43.69 Å
总原子数 total_atoms	3715
残基数 n_residues	450
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	108.2 Å
Rg (实空间) rg_real	37.07 Å
Rg 误差 (实空间) rg_real_error	0.42 Å
I(0) (实空间) i0_real	4.7640e+07
I(0) 误差 (实空间) i0_real_error	6.7000e+05
Rg (倒空间) rg_reciprocal	41.59 Å
I(0) (倒空间) i0_reciprocal	50340000.0000
解质量估计 total_estimate	0.6372
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	28.5 Å
偏度 Skewness skewness	0.415
峰度 Kurtosis kurtosis	-0.772
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.7688
最高正则化参数 α highest_alpha	1915000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.008; Oscil: 0.901; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.653; 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	VIMENTIN
分子量 formula_weight	9920.1 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	4169

CEVDALKGTNESLERQMREMEENFAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRI

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	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	454

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1gk4a_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.20 — Intermediate filament protein, coiled coil region
家族 Family family	h.1.20.1 — Intermediate filament protein, coiled coil region

结构域编号 domain_id	d1gk4b_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.20 — Intermediate filament protein, coiled coil region
家族 Family family	h.1.20.1 — Intermediate filament protein, coiled coil region

结构域编号 domain_id	d1gk4c_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.20 — Intermediate filament protein, coiled coil region
家族 Family family	h.1.20.1 — Intermediate filament protein, coiled coil region

结构域编号 domain_id	d1gk4d_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.20 — Intermediate filament protein, coiled coil region
家族 Family family	h.1.20.1 — Intermediate filament protein, coiled coil region

结构域编号 domain_id	d1gk4e_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.20 — Intermediate filament protein, coiled coil region
家族 Family family	h.1.20.1 — Intermediate filament protein, coiled coil region

结构域编号 domain_id	d1gk4f_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.20 — Intermediate filament protein, coiled coil region
家族 Family family	h.1.20.1 — Intermediate filament protein, coiled coil region

CATH v4.4 (6 domains)

结构域编号 domain_id	1gk4A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1gk4B00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1gk4C00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1gk4D00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1gk4E00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1gk4F00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	170 —

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7. 引用文献 (3)

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晶胞边长 a length_a	76.594 Å
晶胞边长 b length_b	84.283 Å
晶胞边长 c length_c	240.785 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	48

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	34.520 Å
R 因子 r_factor	0.2420
R_work r_work	0.2420
R_free r_free	0.2620

fit	/app/data/saxs_computation/gk/1gk4/1gk4.fit
pddf	/app/data/pr_computation/gk/1gk4/1gk4.pr.out
profile	/app/data/saxs_computation/gk/1gk4/1gk4.dat