SAXSdb — 1jvm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1jvm
沉积日期 deposition_date	2001-08-30
结构标题 title	KCSA POTASSIUM CHANNEL WITH TBA (TETRABUTYLAMMONIUM) AND RUBIDIUM
关键词 keywords	MEMBRANE PROTEIN, POTASSIUM CHANNEL, METAL TRANSPORT; MEMBRANE 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	21.68 Å
回转半径 Rg (电子) rg_electron	20.52 Å
零角强度 I(0) i0	23084600.00
分子量 molecular_weight	40195.0 kDa
排除体积 excluded_volume	51732 Å³
包络体积 envelope_volume	58172 Å³
水化壳体积 shell_volume	23233 Å³
包络直径 envelope_diameter	68.6 Å
壳层 Rg shell_rg	27.72 Å
包络 Rg envelope_rg	21.01 Å
形状 Rg shape_rg	20.58 Å
总 Rg total_rg	21.34 Å
总原子数 total_atoms	2834
残基数 n_residues	394
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	67.5 Å
Rg (实空间) rg_real	21.59 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	2.3080e+07
I(0) 误差 (实空间) i0_real_error	2.8140e+05
Rg (倒空间) rg_reciprocal	21.61 Å
I(0) (倒空间) i0_reciprocal	23080000.0000
解质量估计 total_estimate	0.9081
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	27.2 Å
偏度 Skewness skewness	0.210
峰度 Kurtosis kurtosis	-0.439
角度范围 angular_range	— – 0.3650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5454000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

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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	Voltage-gated potassium channel
分子量 formula_weight	13358.8 kDa
突变 mutation	P2A,L90C
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	A,B,C,D
原子数 atom_count	2835

MAPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQERRGHF

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 2 non-polymer

描述 description	RUBIDIUM ION
分子量 formula_weight	85.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 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 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	1

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1jvma_
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

结构域编号 domain_id	d1jvmb_
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

结构域编号 domain_id	d1jvmc_
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

结构域编号 domain_id	d1jvmd_
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 (4 domains)

结构域编号 domain_id	1jvmA00
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 —

结构域编号 domain_id	1jvmB00
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 —

结构域编号 domain_id	1jvmC00
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 —

结构域编号 domain_id	1jvmD00
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	129.800 Å
晶胞边长 b length_b	69.400 Å
晶胞边长 c length_c	112.700 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	125.60 °
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	2.800 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2900
R_work r_work	0.2810
R_free r_free	0.3021

fit	/app/data/saxs_computation/jv/1jvm/1jvm.fit
pddf	/app/data/pr_computation/jv/1jvm/1jvm.pr.out
profile	/app/data/saxs_computation/jv/1jvm/1jvm.dat

KCSA POTASSIUM CHANNEL WITH TBA (TETRABUTYLAMMONIUM) AND RUBIDIUM

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 non-polymer

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)