2jk5

Potassium Channel KcsA in complex with Tetrabutylammonium in high K

Method: X-RAY DIFFRACTION D_max: 80.7 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	2jk5
沉积日期 deposition_date	2008-08-15
结构标题 title	Potassium Channel KcsA in complex with Tetrabutylammonium in high K
关键词 keywords	IMMUNE SYSTEM-METAL TRANSPORT COMPLEX, QUATERNARY AMMONIUM, PROTEIN-ANTIBODY FAB COMPLEX, IONIC CHANNEL, ION TRANSPORT; IMMUNE SYSTEM/METAL TRANSPORT
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	30.46 Å
回转半径 Rg (电子) rg_electron	31.11 Å
零角强度 I(0) i0	53083700.00
分子量 molecular_weight	58608.0 kDa
排除体积 excluded_volume	73797 Å³
包络体积 envelope_volume	95881 Å³
水化壳体积 shell_volume	28576 Å³
包络直径 envelope_diameter	130.9 Å
壳层 Rg shell_rg	34.23 Å
包络 Rg envelope_rg	32.54 Å
形状 Rg shape_rg	31.02 Å
总 Rg total_rg	31.69 Å
总原子数 total_atoms	4120
残基数 n_residues	534
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	80.7 Å
Rg (实空间) rg_real	27.56 Å
Rg 误差 (实空间) rg_real_error	0.20 Å
I(0) (实空间) i0_real	5.0160e+07
I(0) 误差 (实空间) i0_real_error	6.3600e+05
Rg (倒空间) rg_reciprocal	30.87 Å
I(0) (倒空间) i0_reciprocal	53070000.0000
解质量估计 total_estimate	0.6840
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	31.0 Å
偏度 Skewness skewness	0.381
峰度 Kurtosis kurtosis	-0.443
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	1.3490
最高正则化参数 α highest_alpha	5082000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.004; Oscil: 0.982; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.986; 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 (10)

Entity 1 polymer

描述 description	ANTIBODY FAB FRAGMENT LIGHT CHAIN
分子量 formula_weight	23411.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4420

QVQLQQPGAELVKPGASVKLSCKASGYTFTSDWIHWVKQRPGHGLEWIGEIIPSYGRANYNEKIQKKATLTADKSSSTAFMQLSSLTSEDSAVYYCARERGDGYFAVWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRD

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	MUS MUSCULUS

Entity 2 polymer

描述 description	ANTIBODY FAB FRAGMENT HEAVY CHAIN
分子量 formula_weight	23435.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

DILLTQSPAILSVSPGERVSFSCRASQSIGTDIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIANYYCQQSNRWPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	MUS MUSCULUS

Entity 3 polymer

描述 description	VOLTAGE-GATED POTASSIUM CHANNEL
分子量 formula_weight	13237.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

MPPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQERRGH

来源 Source

来源生物 organism	STREPTOMYCES LIVIDANS
NCBI 分类编号 ncbi_taxonomy_id	1916
宿主生物 host_organism	ESCHERICHIA COLI

Entity 4 non-polymer

描述 description	COBALT (II) ION
分子量 formula_weight	58.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 6 non-polymer

描述 description	NONAN-1-OL
分子量 formula_weight	144.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	(2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE
分子量 formula_weight	414.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	TETRABUTYLAMMONIUM ION
分子量 formula_weight	242.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 non-polymer

描述 description	HEPTANE
分子量 formula_weight	100.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 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	204

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6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d2jk5a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2jk5a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d2jk5a3
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	d2jk5b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d2jk5b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d2jk5c_
类 Class class	f — Membrane and cell surface proteins and peptides
折叠类型 Fold fold	f.14 — Gated ion channels
超家族 Superfamily superfamily	f.14.1 — Voltage-gated ion channels
家族 Family family	f.14.1.1 — Voltage-gated potassium channels

CATH v4.4 (5 domains)

结构域编号 domain_id	2jk5A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2jk5A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2jk5B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2jk5B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	2jk5C00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	70 —

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7. 引用文献 (1)

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晶胞边长 a length_a	156.145 Å
晶胞边长 b length_b	156.145 Å
晶胞边长 c length_c	76.326 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	8

空间群 space_group	I 4
空间群编号 int_tables_number	79
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2050
R_work r_work	0.2020
R_free r_free	0.2490

fit	/app/data/saxs_computation/jk/2jk5/2jk5.fit
pddf	/app/data/pr_computation/jk/2jk5/2jk5.pr.out
profile	/app/data/saxs_computation/jk/2jk5/2jk5.dat

Potassium Channel KcsA in complex with Tetrabutylammonium in high K

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 (10)

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 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)