2fg0

;Crystal structure of a putative gamma-d-glutamyl-l-diamino acid endopeptidase (npun_r0659) from nostoc punctiforme pcc 73102 at 1.79 A resolution ;

Method: X-RAY DIFFRACTION D_max: 90.6 Å Quality: GOOD

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	2fg0
沉积日期 deposition_date	2005-12-20
结构标题 title	;Crystal structure of a putative gamma-d-glutamyl-l-diamino acid endopeptidase (npun_r0659) from nostoc punctiforme pcc 73102 at 1.79 A resolution ;
关键词 keywords	Nlpc/p60 family, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, hydrolase; HYDROLASE
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	25.70 Å
回转半径 Rg (电子) rg_electron	25.16 Å
零角强度 I(0) i0	40738900.00
分子量 molecular_weight	48933.0 kDa
排除体积 excluded_volume	60782 Å³
包络体积 envelope_volume	72812 Å³
水化壳体积 shell_volume	25287 Å³
包络直径 envelope_diameter	91.7 Å
壳层 Rg shell_rg	31.20 Å
包络 Rg envelope_rg	25.60 Å
形状 Rg shape_rg	25.20 Å
总 Rg total_rg	25.69 Å
总原子数 total_atoms	3444
残基数 n_residues	440
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	90.6 Å
Rg (实空间) rg_real	25.85 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	4.0740e+07
I(0) 误差 (实空间) i0_real_error	5.8600e+05
Rg (倒空间) rg_reciprocal	25.80 Å
I(0) (倒空间) i0_reciprocal	40740000.0000
解质量估计 total_estimate	0.8516
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.3 Å
偏度 Skewness skewness	0.553
峰度 Kurtosis kurtosis	0.023
角度范围 angular_range	— – 0.3100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10850000.0000
实空间数据点数 n_real_points	63
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.876; Smooth: 0.963

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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	COG0791: Cell wall-associated hydrolases (invasion-associated proteins)
分子量 formula_weight	27591.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	3977

MGSDKIHHHHHHMVRLSEAEVQNPKLGEYQCLADLNLFDSPECTRLATQSASGRHLWVTSNHQNLAVEVYLCEDDYPGWLSLSDFDSLQPATVPYQAATFSESEIKKLLAEVIAFTQKAMQQSNYYLWGGTVGPNYDCSGLMQAAFASVGIWLPRDAYQQEGFTQPITIAELVAGDLVFFGTSQKATHVGLYLADGYYIHSSGKDQGRDGIGIDILSEQGDAVSLSYYQQLRGAGRVFKSYEPQRR

来源 Source

来源生物 organism	Nostoc punctiforme
NCBI 分类编号 ncbi_taxonomy_id	63737
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 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	428

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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	d2fg0a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.11 — Prokaryotic SH3-related domain
家族 Family family	b.34.11.3 — Spr N-terminal domain-like

结构域编号 domain_id	d2fg0a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.3 — Cysteine proteinases
超家族 Superfamily superfamily	d.3.1 — Cysteine proteinases
家族 Family family	d.3.1.16 — NlpC/P60

结构域编号 domain_id	d2fg0b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.11 — Prokaryotic SH3-related domain
家族 Family family	b.34.11.3 — Spr N-terminal domain-like

结构域编号 domain_id	d2fg0b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.3 — Cysteine proteinases
超家族 Superfamily superfamily	d.3.1 — Cysteine proteinases
家族 Family family	d.3.1.16 — NlpC/P60

CATH v4.4 (4 domains)

结构域编号 domain_id	2fg0A01
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	40 — SH3 Domains

结构域编号 domain_id	2fg0A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1720 — endopeptidase fold (from Nostoc punctiforme)
同源超家族 H-superfamily homologous superfamily	10 — endopeptidase domain like (from Nostoc punctiforme)

结构域编号 domain_id	2fg0B01
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	40 — SH3 Domains

结构域编号 domain_id	2fg0B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1720 — endopeptidase fold (from Nostoc punctiforme)
同源超家族 H-superfamily homologous superfamily	10 — endopeptidase domain like (from Nostoc punctiforme)

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7. 引用文献 (1)

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晶胞边长 a length_a	125.080 Å
晶胞边长 b length_b	125.080 Å
晶胞边长 c length_c	97.670 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	16

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	1.790 Å
最低分辨率 resolution_low	29.480 Å
R 因子 r_factor	—
R_work r_work	0.1540
R_free r_free	0.1720

fit	/app/data/saxs_computation/fg/2fg0/2fg0.fit
pddf	/app/data/pr_computation/fg/2fg0/2fg0.pr.out
profile	/app/data/saxs_computation/fg/2fg0/2fg0.dat