1jcc

Crystal Structure of a Novel Alanine-Zipper Trimer at 1.7 A Resolution, V13A,L16A,V20A,L23A,V27A,M30A,V34A mutations

Method: X-RAY DIFFRACTION D_max: 48.8 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	1jcc
沉积日期 deposition_date	2001-06-08
结构标题 title	Crystal Structure of a Novel Alanine-Zipper Trimer at 1.7 A Resolution, V13A,L16A,V20A,L23A,V27A,M30A,V34A mutations
关键词 keywords	LIPOPROTEIN, PROTEIN FOLDING, COILED COIL, HELIX CAPPING, ALANINE-ZIPPER, MEMBRANE PROTEIN; 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	23.12 Å
回转半径 Rg (电子) rg_electron	23.70 Å
零角强度 I(0) i0	6661770.00
分子量 molecular_weight	15858.0 kDa
排除体积 excluded_volume	18501 Å³
包络体积 envelope_volume	24777 Å³
水化壳体积 shell_volume	10921 Å³
包络直径 envelope_diameter	88.2 Å
壳层 Rg shell_rg	26.14 Å
包络 Rg envelope_rg	24.68 Å
形状 Rg shape_rg	23.51 Å
总 Rg total_rg	24.49 Å
总原子数 total_atoms	1097
残基数 n_residues	156
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	48.8 Å
Rg (实空间) rg_real	17.75 Å
Rg 误差 (实空间) rg_real_error	0.08 Å
I(0) (实空间) i0_real	5.5320e+06
I(0) 误差 (实空间) i0_real_error	4.4180e+04
Rg (倒空间) rg_reciprocal	23.57 Å
I(0) (倒空间) i0_reciprocal	6661000.0000
解质量估计 total_estimate	0.5828
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	15.0 Å
偏度 Skewness skewness	0.342
峰度 Kurtosis kurtosis	-0.784
角度范围 angular_range	— – 0.3450 Å⁻¹
当前正则化参数 α current_alpha	7.1150
最高正则化参数 α highest_alpha	821000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.012; Oscil: 0.967; Stabil: 0.947; Sysdev: 0.000; Positv: 1.000; Valcen: 0.835; 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	MAJOR OUTER MEMBRANE LIPOPROTEIN
分子量 formula_weight	5905.2 kDa
突变 mutation	V13A,L16A,V20A,L23A,V27A,M30A,V34A
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	1331

SSNAKIDQLSSDAQTANAKADQASNDANAARSDAQAAKDDAARANQRLDNMATKYR

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	234

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1jcca_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.16 — Outer membrane lipoprotein
家族 Family family	h.1.16.1 — Outer membrane lipoprotein

结构域编号 domain_id	d1jccb_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.16 — Outer membrane lipoprotein
家族 Family family	h.1.16.1 — Outer membrane lipoprotein

结构域编号 domain_id	d1jccc_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.16 — Outer membrane lipoprotein
家族 Family family	h.1.16.1 — Outer membrane lipoprotein

CATH v4.4 (3 domains)

结构域编号 domain_id	1jccA00
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	190 —

结构域编号 domain_id	1jccB00
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	190 —

结构域编号 domain_id	1jccC00
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	190 —

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7. 引用文献 (1)

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晶胞边长 a length_a	62.388 Å
晶胞边长 b length_b	33.322 Å
晶胞边长 c length_c	71.979 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.55 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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	1.700 Å
最低分辨率 resolution_low	35.130 Å
R 因子 r_factor	—
R_work r_work	0.1920
R_free r_free	0.2230

fit	/app/data/saxs_computation/jc/1jcc/1jcc.fit
pddf	/app/data/pr_computation/jc/1jcc/1jcc.pr.out
profile	/app/data/saxs_computation/jc/1jcc/1jcc.dat

Crystal Structure of a Novel Alanine-Zipper Trimer at 1.7 A Resolution, V13A,L16A,V20A,L23A,V27A,M30A,V34A mutations

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)