SAXSdb — 1xml

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1xml
沉积日期 deposition_date	2004-10-04
结构标题 title	Structure of human Dcps
关键词 keywords	scavenger Decapping Enzyme, CHAPERONE; CHAPERONE
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	27.49 Å
回转半径 Rg (电子) rg_electron	26.26 Å
零角强度 I(0) i0	72041400.00
分子量 molecular_weight	66807.0 kDa
排除体积 excluded_volume	84058 Å³
包络体积 envelope_volume	107970 Å³
水化壳体积 shell_volume	33828 Å³
包络直径 envelope_diameter	79.1 Å
壳层 Rg shell_rg	33.93 Å
包络 Rg envelope_rg	25.62 Å
形状 Rg shape_rg	26.26 Å
总 Rg total_rg	27.12 Å
总原子数 total_atoms	4723
残基数 n_residues	566
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	79.7 Å
Rg (实空间) rg_real	27.26 Å
Rg 误差 (实空间) rg_real_error	0.32 Å
I(0) (实空间) i0_real	7.2040e+07
I(0) 误差 (实空间) i0_real_error	9.3000e+05
Rg (倒空间) rg_reciprocal	27.33 Å
I(0) (倒空间) i0_reciprocal	72050000.0000
解质量估计 total_estimate	0.9142
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	37.1 Å
偏度 Skewness skewness	0.017
峰度 Kurtosis kurtosis	-0.619
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15810000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.965

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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	heat shock-like protein 1
分子量 formula_weight	39110.3 kDa
突变 mutation	L206M, L317M
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	5177

GPLGSMADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDMKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTMTFALRADDPLLKLLQEAQQS

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 BL21(DE3)

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	454

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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	d1xmla1
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	d1xmla2
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.246.1.0 — automated matches

结构域编号 domain_id	d1xmlb1
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	d1xmlb2
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.246.1.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	1xmlA01
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	1xmlA02
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	1xmlB01
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	1xmlB02
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	101.922 Å
晶胞边长 b length_b	103.863 Å
晶胞边长 c length_c	71.067 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 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2211
R_work r_work	0.2195
R_free r_free	0.2526

fit	/app/data/saxs_computation/xm/1xml/1xml.fit
pddf	/app/data/pr_computation/xm/1xml/1xml.pr.out
profile	/app/data/saxs_computation/xm/1xml/1xml.dat

Structure of human Dcps

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