SAXSdb — 1i0x

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1i0x
沉积日期 deposition_date	2001-01-30
结构标题 title	;RIBONUCLEASE T1 IN COMPLEX WITH 2'GMP (FORM II CRYSTAL) ;
关键词 keywords	;Ribonuclease, RNase, metal binding, stability, 2'GMP, 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	28.36 Å
回转半径 Rg (电子) rg_electron	28.26 Å
零角强度 I(0) i0	43335800.00
分子量 molecular_weight	45924.0 kDa
排除体积 excluded_volume	54889 Å³
包络体积 envelope_volume	72171 Å³
水化壳体积 shell_volume	23676 Å³
包络直径 envelope_diameter	99.4 Å
壳层 Rg shell_rg	32.07 Å
包络 Rg envelope_rg	27.90 Å
形状 Rg shape_rg	28.25 Å
总 Rg total_rg	28.67 Å
总原子数 total_atoms	3221
残基数 n_residues	415
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	96.4 Å
Rg (实空间) rg_real	28.64 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	4.3340e+07
I(0) 误差 (实空间) i0_real_error	6.8140e+05
Rg (倒空间) rg_reciprocal	28.55 Å
I(0) (倒空间) i0_reciprocal	43330000.0000
解质量估计 total_estimate	0.8035
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	39.6 Å
偏度 Skewness skewness	0.543
峰度 Kurtosis kurtosis	-0.020
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10550000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.696; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.798; Smooth: 0.559

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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	GUANYL-SPECIFIC RIBONUCLEASE T1
分子量 formula_weight	11094.7 kDa
EC 编号 ec_number	3.1.27.3
突变 mutation	Q25K
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	3750

ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT

来源 Source

来源生物 organism	Aspergillus oryzae
NCBI 分类编号 ncbi_taxonomy_id	5062
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	GUANOSINE-2'-MONOPHOSPHATE
分子量 formula_weight	363.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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	529

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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	d1i0xa_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.1 — Microbial ribonucleases
超家族 Superfamily superfamily	d.1.1 — Microbial ribonucleases
家族 Family family	d.1.1.4 — Fungal ribonucleases

结构域编号 domain_id	d1i0xb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.1 — Microbial ribonucleases
超家族 Superfamily superfamily	d.1.1 — Microbial ribonucleases
家族 Family family	d.1.1.4 — Fungal ribonucleases

结构域编号 domain_id	d1i0xc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.1 — Microbial ribonucleases
超家族 Superfamily superfamily	d.1.1 — Microbial ribonucleases
家族 Family family	d.1.1.4 — Fungal ribonucleases

结构域编号 domain_id	d1i0xd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.1 — Microbial ribonucleases
超家族 Superfamily superfamily	d.1.1 — Microbial ribonucleases
家族 Family family	d.1.1.4 — Fungal ribonucleases

CATH v4.4 (4 domains)

结构域编号 domain_id	1i0xA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	30 — Microbial ribonucleases

结构域编号 domain_id	1i0xB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	30 — Microbial ribonucleases

结构域编号 domain_id	1i0xC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	30 — Microbial ribonucleases

结构域编号 domain_id	1i0xD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily	30 — Microbial ribonucleases

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7. 引用文献 (1)

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晶胞边长 a length_a	58.271 Å
晶胞边长 b length_b	59.696 Å
晶胞边长 c length_c	100.136 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 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.650 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	0.1921
R_work r_work	0.1903
R_free r_free	0.2160

fit	/app/data/saxs_computation/i0/1i0x/1i0x.fit
pddf	/app/data/pr_computation/i0/1i0x/1i0x.pr.out
profile	/app/data/saxs_computation/i0/1i0x/1i0x.dat

;RIBONUCLEASE T1 IN COMPLEX WITH 2'GMP (FORM II CRYSTAL) ;

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)