SAXSdb — 1r7m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r7m
沉积日期 deposition_date	2003-10-21
结构标题 title	The homing endonuclease I-SceI bound to its DNA recognition region
关键词 keywords	protein-DNA complex, endonuclease, LAGLIDADG, BETA-SADDLE, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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	31.70 Å
回转半径 Rg (电子) rg_electron	31.22 Å
零角强度 I(0) i0	154337000.00
分子量 molecular_weight	82584.0 kDa
排除体积 excluded_volume	96039 Å³
包络体积 envelope_volume	125450 Å³
水化壳体积 shell_volume	35202 Å³
包络直径 envelope_diameter	117.8 Å
壳层 Rg shell_rg	36.13 Å
包络 Rg envelope_rg	31.63 Å
形状 Rg shape_rg	31.15 Å
总 Rg total_rg	31.73 Å
总原子数 total_atoms	5682
残基数 n_residues	542
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	113.2 Å
Rg (实空间) rg_real	32.03 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	1.5430e+08
I(0) 误差 (实空间) i0_real_error	2.7550e+06
Rg (倒空间) rg_reciprocal	31.89 Å
I(0) (倒空间) i0_reciprocal	154300000.0000
解质量估计 total_estimate	0.8283
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	34.0 Å
偏度 Skewness skewness	0.641
峰度 Kurtosis kurtosis	0.138
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12010000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.880; Smooth: 0.778

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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 (5)

Entity 1 polymer

描述 description	5'-D(CPAPCPGPCPTPAPGPGPGPAPTPAPAPCPAPGPGPGPTPAPAPTPAP*C)-3'
分子量 formula_weight	7741.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C,E
原子数 atom_count	5883

CACGCTAGGGATAACAGGGTAATAC

Entity 2 polymer

描述 description	5'-D(GPGPTPAPTPTPAPCPCPCPTPGPTPTPAPTPCPCPCPTPAPGPCPGP*T)-3'
分子量 formula_weight	7615.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D,F

GGTATTACCCTGTTATCCCTAGCGT

Entity 3 polymer

描述 description	Intron-encoded endonuclease I-SceI
分子量 formula_weight	27717.2 kDa
EC 编号 ec_number	3.1.-.-
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

MKNIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNKSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLPNTISSETFLK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 4 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	6

Entity 5 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	201

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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	d1r7ma1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.95 — Homing endonuclease-like
超家族 Superfamily superfamily	d.95.2 — Homing endonucleases
家族 Family family	d.95.2.1 — Group I mobile intron endonuclease

结构域编号 domain_id	d1r7ma2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.95 — Homing endonuclease-like
超家族 Superfamily superfamily	d.95.2 — Homing endonucleases
家族 Family family	d.95.2.1 — Group I mobile intron endonuclease

结构域编号 domain_id	d1r7mb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.95 — Homing endonuclease-like
超家族 Superfamily superfamily	d.95.2 — Homing endonucleases
家族 Family family	d.95.2.1 — Group I mobile intron endonuclease

结构域编号 domain_id	d1r7mb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.95 — Homing endonuclease-like
超家族 Superfamily superfamily	d.95.2 — Homing endonucleases
家族 Family family	d.95.2.1 — Group I mobile intron endonuclease

CATH v4.4 (4 domains)

结构域编号 domain_id	1r7mA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

结构域编号 domain_id	1r7mA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

结构域编号 domain_id	1r7mB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

结构域编号 domain_id	1r7mB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

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7. 引用文献 (1)

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晶胞边长 a length_a	80.600 Å
晶胞边长 b length_b	90.700 Å
晶胞边长 c length_c	115.300 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	8

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	2.250 Å
最低分辨率 resolution_low	24.350 Å
R 因子 r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.2670

fit	/app/data/saxs_computation/r7/1r7m/1r7m.fit
pddf	/app/data/pr_computation/r7/1r7m/1r7m.pr.out
profile	/app/data/saxs_computation/r7/1r7m/1r7m.dat

The homing endonuclease I-SceI bound to its DNA recognition region

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 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)