1nmp

Structural genomics, ybgI protein, unknown function

Method: X-RAY DIFFRACTION D_max: 117.2 Å Quality: EXCELLENT

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	1nmp
沉积日期 deposition_date	2003-01-10
结构标题 title	Structural genomics, ybgI protein, unknown function
关键词 keywords	ybgI, hypothetical protein, toroidal structure, Structure 2 Function Project, S2F, Structural Genomics, unknown function; structural genomics, unknown function
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	37.80 Å
回转半径 Rg (电子) rg_electron	37.15 Å
零角强度 I(0) i0	399519000.00
分子量 molecular_weight	161550.0 kDa
排除体积 excluded_volume	201810 Å³
包络体积 envelope_volume	269360 Å³
水化壳体积 shell_volume	59280 Å³
包络直径 envelope_diameter	123.9 Å
壳层 Rg shell_rg	44.59 Å
包络 Rg envelope_rg	36.21 Å
形状 Rg shape_rg	37.14 Å
总 Rg total_rg	37.67 Å
总原子数 total_atoms	11393
残基数 n_residues	1482
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	117.2 Å
Rg (实空间) rg_real	37.60 Å
Rg 误差 (实空间) rg_real_error	1.04 Å
I(0) (实空间) i0_real	3.9950e+08
I(0) 误差 (实空间) i0_real_error	7.7680e+06
Rg (倒空间) rg_reciprocal	37.73 Å
I(0) (倒空间) i0_reciprocal	399600000.0000
解质量估计 total_estimate	0.9052
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	44.7 Å
偏度 Skewness skewness	0.130
峰度 Kurtosis kurtosis	-0.570
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30590000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.940

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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	Hypothetical protein ybgI
分子量 formula_weight	26919.4 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	11969

MKNTELEQLINEKLNSAAISDYAPNGLQVEGKETVQKIVTGVTASQALLDEAVRLGADAVIVHHGYFWKGESPVIRGMKRNRLKTLLANDINLYGWHLPLDAHPELGNNAQLAALLGITVMGEIEPLVPWGELTMPVPGLELASWIEARLGRKPLWCGDTGPEVVQRVAWCTGGGQSFIDSAARFGVDAFITGEVSEQTIHSAREQGLHFYAAGHHATERGGIRALSEWLNENTDLDVTFIDIPNPA

来源 Source

来源生物 organism	Escherichia coli, Escherichia coli O157:H7
通用名 common_name	,
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	11

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	576

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1nmpa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmpb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmpc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmpd_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmpe_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	d1nmpf_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
超家族 Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
家族 Family family	c.135.1.1 — NIF3 (NGG1p interacting factor 3)-like

CATH v4.4 (12 domains)

结构域编号 domain_id	1nmpA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

结构域编号 domain_id	1nmpF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

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7. 引用文献 (1)

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晶胞边长 a length_a	156.730 Å
晶胞边长 b length_b	156.730 Å
晶胞边长 c length_c	57.610 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	120.00 °
晶胞分子数 Z z_pdb	18

空间群 space_group	P 3
空间群编号 int_tables_number	143
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	19.760 Å
R 因子 r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2530

fit	/app/data/saxs_computation/nm/1nmp/1nmp.fit
pddf	/app/data/pr_computation/nm/1nmp/1nmp.pr.out
profile	/app/data/saxs_computation/nm/1nmp/1nmp.dat