1j1d

Crystal structure of the 46kDa domain of human cardiac troponin in the Ca2+ saturated form

Method: X-RAY DIFFRACTION D_max: 147.0 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	1j1d
沉积日期 deposition_date	2002-12-03
结构标题 title	Crystal structure of the 46kDa domain of human cardiac troponin in the Ca2+ saturated form
关键词 keywords	Thin filament, muscle regulation, Ca2+ binding protein, EF-hand, coiled-coil, CONTRACTILE PROTEIN; CONTRACTILE 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	39.44 Å
回转半径 Rg (电子) rg_electron	39.94 Å
零角强度 I(0) i0	107066000.00
分子量 molecular_weight	81089.0 kDa
排除体积 excluded_volume	100970 Å³
包络体积 envelope_volume	154070 Å³
水化壳体积 shell_volume	35563 Å³
包络直径 envelope_diameter	153.2 Å
壳层 Rg shell_rg	40.69 Å
包络 Rg envelope_rg	39.42 Å
形状 Rg shape_rg	39.88 Å
总 Rg total_rg	40.19 Å
总原子数 total_atoms	5675
残基数 n_residues	698
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	147.0 Å
Rg (实空间) rg_real	40.02 Å
Rg 误差 (实空间) rg_real_error	2.08 Å
I(0) (实空间) i0_real	1.0710e+08
I(0) 误差 (实空间) i0_real_error	2.2050e+06
Rg (倒空间) rg_reciprocal	39.66 Å
I(0) (倒空间) i0_reciprocal	107000000.0000
解质量估计 total_estimate	0.8011
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	40.4 Å
偏度 Skewness skewness	0.617
峰度 Kurtosis kurtosis	0.059
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6606000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.678; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.667; Smooth: 0.708

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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 (5)

Entity 1 polymer

描述 description	Troponin C
分子量 formula_weight	18401.4 kDa
突变 mutation	C35S, C84S
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D
原子数 atom_count	5777

MDDIYKAAVEQLTEEQKNEFKAAFDIFVLGAEDGSISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRSMKDDSKGKSEEELSDLFRMFDKNADGYIDLEELKIMLQATGETITEDDIEELMKDGDKNNDGRIDYDEFLEFMKGVE

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	Troponin T
分子量 formula_weight	12842.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E

HFGGYIQKQAQTERKSGKRQTEREKKKKILAERRKVLAIDHLNEDQLREKAKELWQTIYNLEAEKFDLQEKFKQQKYEINVLRNRINDNQKVSKTRGKAKVTGRWK

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	Troponin I
分子量 formula_weight	15191.7 kDa
突变 mutation	T31M, C80A, C97A
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,F

MEPHAKKKSKISASRKLQLKTLLLQIAKQELEREAEERRGEKGRALSTRAQPLELAGLGFAELQDLARQLHARVDKVDEERYDIEAKVTKNITEIADLTQKIFDLRGKFKRPTLRRVRISADAMMQALLGARA

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 4 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	6

Entity 5 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	102

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1j1da_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.39 — EF Hand-like
超家族 Superfamily superfamily	a.39.1 — EF-hand
家族 Family family	a.39.1.5 — Calmodulin-like

结构域编号 domain_id	d1j1db_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.25 — Troponin coil-coiled subunits
家族 Family family	h.1.25.1 — Troponin T

结构域编号 domain_id	d1j1dc_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.25 — Troponin coil-coiled subunits
家族 Family family	h.1.25.2 — Troponin I

结构域编号 domain_id	d1j1dd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.39 — EF Hand-like
超家族 Superfamily superfamily	a.39.1 — EF-hand
家族 Family family	a.39.1.5 — Calmodulin-like

结构域编号 domain_id	d1j1de_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.25 — Troponin coil-coiled subunits
家族 Family family	h.1.25.1 — Troponin T

结构域编号 domain_id	d1j1df_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.25 — Troponin coil-coiled subunits
家族 Family family	h.1.25.2 — Troponin I

CATH v4.4 (8 domains)

结构域编号 domain_id	1j1dA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1j1dA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1j1dB00
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	350 — Troponin complex, TnI/TnT subunit

结构域编号 domain_id	1j1dC01
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	350 — Troponin complex, TnI/TnT subunit

结构域编号 domain_id	1j1dD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1j1dD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	1j1dE00
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	350 — Troponin complex, TnI/TnT subunit

结构域编号 domain_id	1j1dF01
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	350 — Troponin complex, TnI/TnT subunit

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7. 引用文献 (3)

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晶胞边长 a length_a	42.346 Å
晶胞边长 b length_b	167.860 Å
晶胞边长 c length_c	69.707 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.35 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.610 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	—
R_work r_work	0.2640
R_free r_free	0.2980

fit	/app/data/saxs_computation/j1/1j1d/1j1d.fit
pddf	/app/data/pr_computation/j1/1j1d/1j1d.pr.out
profile	/app/data/saxs_computation/j1/1j1d/1j1d.dat

Crystal structure of the 46kDa domain of human cardiac troponin in the Ca2+ saturated 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 (5)

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 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)