SAXSdb — 1st0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1st0
沉积日期 deposition_date	2004-03-24
结构标题 title	Structure of DcpS bound to m7GpppG
关键词 keywords	RNA DECAY, EXOSOME, DECAPPING, HIT PROTEIN, MESSENGER RNA, MRNA, CAP, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	26.55 Å
回转半径 Rg (电子) rg_electron	25.31 Å
零角强度 I(0) i0	84297700.00
分子量 molecular_weight	71057.0 kDa
排除体积 excluded_volume	88537 Å³
包络体积 envelope_volume	107080 Å³
水化壳体积 shell_volume	34302 Å³
包络直径 envelope_diameter	85.2 Å
壳层 Rg shell_rg	33.43 Å
包络 Rg envelope_rg	25.28 Å
形状 Rg shape_rg	25.28 Å
总 Rg total_rg	26.25 Å
总原子数 total_atoms	5004
残基数 n_residues	597
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	82.3 Å
Rg (实空间) rg_real	26.40 Å
Rg 误差 (实空间) rg_real_error	0.50 Å
I(0) (实空间) i0_real	8.4300e+07
I(0) 误差 (实空间) i0_real_error	1.2160e+06
Rg (倒空间) rg_reciprocal	26.45 Å
I(0) (倒空间) i0_reciprocal	84300000.0000
解质量估计 total_estimate	0.9050
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	34.3 Å
偏度 Skewness skewness	0.151
峰度 Kurtosis kurtosis	-0.504
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21200000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.991

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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	mRNA decapping enzyme
分子量 formula_weight	38638.7 kDa
突变 mutation	HIS277ASN
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	B,A
原子数 atom_count	5647

MADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLNVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
分子量 formula_weight	803.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	YTTRIUM (III) ION
分子量 formula_weight	88.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	643

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1st0a1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.13 — HIT-like
超家族 Superfamily superfamily	d.13.1 — HIT-like
家族 Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

结构域编号 domain_id	d1st0a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
超家族 Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
家族 Family family	d.246.1.1 — mRNA decapping enzyme DcpS N-terminal domain

结构域编号 domain_id	d1st0b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.13 — HIT-like
超家族 Superfamily superfamily	d.13.1 — HIT-like
家族 Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

结构域编号 domain_id	d1st0b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
超家族 Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
家族 Family family	d.246.1.1 — mRNA decapping enzyme DcpS N-terminal domain

CATH v4.4 (5 domains)

结构域编号 domain_id	1st0A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

结构域编号 domain_id	1st0A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	428 — HIT family, subunit A
同源超家族 H-superfamily homologous superfamily	10 — HIT-like

结构域编号 domain_id	1st0B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

结构域编号 domain_id	1st0B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2240 — mRNA decapping enzyme DcpS N-terminal fold
同源超家族 H-superfamily homologous superfamily	10 — mRNA decapping enzyme DcpS N-terminal domain

结构域编号 domain_id	1st0B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	428 — HIT family, subunit A
同源超家族 H-superfamily homologous superfamily	10 — HIT-like

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7. 引用文献 (1)

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晶胞边长 a length_a	59.446 Å
晶胞边长 b length_b	94.783 Å
晶胞边长 c length_c	178.328 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	1.900 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1871
R_free r_free	0.2313

fit	/app/data/saxs_computation/st/1st0/1st0.fit
pddf	/app/data/pr_computation/st/1st0/1st0.pr.out
profile	/app/data/saxs_computation/st/1st0/1st0.dat

Structure of DcpS bound to m7GpppG

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