1npp

CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS NUSG IN P2(1)

Method: X-RAY DIFFRACTION D_max: 130.0 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	1npp
沉积日期 deposition_date	2003-01-18
结构标题 title	CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS NUSG IN P2(1)
关键词 keywords	RNAP transcription factor, NusG, TRANSCRIPTION; TRANSCRIPTION
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	39.88 Å
回转半径 Rg (电子) rg_electron	39.73 Å
零角强度 I(0) i0	167308000.00
分子量 molecular_weight	108620.0 kDa
排除体积 excluded_volume	138330 Å³
包络体积 envelope_volume	209870 Å³
水化壳体积 shell_volume	46444 Å³
包络直径 envelope_diameter	138.1 Å
壳层 Rg shell_rg	42.82 Å
包络 Rg envelope_rg	38.50 Å
形状 Rg shape_rg	39.68 Å
总 Rg total_rg	40.13 Å
总原子数 total_atoms	7628
残基数 n_residues	963
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	130.0 Å
Rg (实空间) rg_real	39.83 Å
Rg 误差 (实空间) rg_real_error	1.13 Å
I(0) (实空间) i0_real	1.6730e+08
I(0) 误差 (实空间) i0_real_error	2.8350e+06
Rg (倒空间) rg_reciprocal	39.87 Å
I(0) (倒空间) i0_reciprocal	167300000.0000
解质量估计 total_estimate	0.6741
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	45.5 Å
偏度 Skewness skewness	0.224
峰度 Kurtosis kurtosis	-0.483
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	8607000.0000
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: 0.919; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 1.000; Smooth: 0.817

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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	Transcription antitermination protein nusG
分子量 formula_weight	28041.7 kDa
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	8486

MSEQQVQELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI

来源 Source

来源生物 organism	Aquifex aeolicus
NCBI 分类编号 ncbi_taxonomy_id	63363
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	ISOPROPYL ALCOHOL
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	858

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1nppa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.114 — N-utilization substance G protein NusG, insert domain
超家族 Superfamily superfamily	b.114.1 — N-utilization substance G protein NusG, insert domain
家族 Family family	b.114.1.1 — N-utilization substance G protein NusG, insert domain

结构域编号 domain_id	d1nppa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.5 — Translation proteins SH3-like domain
家族 Family family	b.34.5.4 — N-utilization substance G protein NusG, C-terminal domain

结构域编号 domain_id	d1nppa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.42 — N-utilization substance G protein NusG, N-terminal domain
家族 Family family	d.58.42.1 — N-utilization substance G protein NusG, N-terminal domain

结构域编号 domain_id	d1nppb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.114 — N-utilization substance G protein NusG, insert domain
超家族 Superfamily superfamily	b.114.1 — N-utilization substance G protein NusG, insert domain
家族 Family family	b.114.1.1 — N-utilization substance G protein NusG, insert domain

结构域编号 domain_id	d1nppb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.5 — Translation proteins SH3-like domain
家族 Family family	b.34.5.4 — N-utilization substance G protein NusG, C-terminal domain

结构域编号 domain_id	d1nppb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.42 — N-utilization substance G protein NusG, N-terminal domain
家族 Family family	d.58.42.1 — N-utilization substance G protein NusG, N-terminal domain

结构域编号 domain_id	d1nppc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.114 — N-utilization substance G protein NusG, insert domain
超家族 Superfamily superfamily	b.114.1 — N-utilization substance G protein NusG, insert domain
家族 Family family	b.114.1.1 — N-utilization substance G protein NusG, insert domain

结构域编号 domain_id	d1nppc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.5 — Translation proteins SH3-like domain
家族 Family family	b.34.5.4 — N-utilization substance G protein NusG, C-terminal domain

结构域编号 domain_id	d1nppc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.42 — N-utilization substance G protein NusG, N-terminal domain
家族 Family family	d.58.42.1 — N-utilization substance G protein NusG, N-terminal domain

结构域编号 domain_id	d1nppd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.114 — N-utilization substance G protein NusG, insert domain
超家族 Superfamily superfamily	b.114.1 — N-utilization substance G protein NusG, insert domain
家族 Family family	b.114.1.1 — N-utilization substance G protein NusG, insert domain

结构域编号 domain_id	d1nppd2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.5 — Translation proteins SH3-like domain
家族 Family family	b.34.5.4 — N-utilization substance G protein NusG, C-terminal domain

结构域编号 domain_id	d1nppd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.42 — N-utilization substance G protein NusG, N-terminal domain
家族 Family family	d.58.42.1 — N-utilization substance G protein NusG, N-terminal domain

CATH v4.4 (12 domains)

结构域编号 domain_id	1nppA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	940 — NusG, N-terminal domain

结构域编号 domain_id	1nppA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	320 — mini-chromosome maintenance (MCM) complex, domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-utilization substance G protein NusG, insert domain

结构域编号 domain_id	1nppA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1nppB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	940 — NusG, N-terminal domain

结构域编号 domain_id	1nppB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	320 — mini-chromosome maintenance (MCM) complex, domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-utilization substance G protein NusG, insert domain

结构域编号 domain_id	1nppB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1nppC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	940 — NusG, N-terminal domain

结构域编号 domain_id	1nppC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	320 — mini-chromosome maintenance (MCM) complex, domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-utilization substance G protein NusG, insert domain

结构域编号 domain_id	1nppC03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	30 —

结构域编号 domain_id	1nppD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	940 — NusG, N-terminal domain

结构域编号 domain_id	1nppD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	320 — mini-chromosome maintenance (MCM) complex, domain 2
同源超家族 H-superfamily homologous superfamily	10 — N-utilization substance G protein NusG, insert domain

结构域编号 domain_id	1nppD03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	30 —

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7. 引用文献 (2)

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晶胞边长 a length_a	87.070 Å
晶胞边长 b length_b	55.860 Å
晶胞边长 c length_c	112.610 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.39 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.000 Å
最低分辨率 resolution_low	19.980 Å
R 因子 r_factor	0.2590
R_work r_work	0.2190
R_free r_free	0.2790

fit	/app/data/saxs_computation/np/1npp/1npp.fit
pddf	/app/data/pr_computation/np/1npp/1npp.pr.out
profile	/app/data/saxs_computation/np/1npp/1npp.dat