1xmm

Structure of human Dcps bound to m7GDP

Method: X-RAY DIFFRACTION D_max: 120.0 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	1xmm
沉积日期 deposition_date	2004-10-04
结构标题 title	Structure of human Dcps bound to m7GDP
关键词 keywords	scavenger decapping enzyme bound m7GDP, 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	37.20 Å
回转半径 Rg (电子) rg_electron	36.82 Å
零角强度 I(0) i0	282030000.00
分子量 molecular_weight	137060.0 kDa
排除体积 excluded_volume	171980 Å³
包络体积 envelope_volume	224280 Å³
水化壳体积 shell_volume	50372 Å³
包络直径 envelope_diameter	119.7 Å
壳层 Rg shell_rg	43.42 Å
包络 Rg envelope_rg	36.24 Å
形状 Rg shape_rg	36.82 Å
总 Rg total_rg	37.22 Å
总原子数 total_atoms	9689
残基数 n_residues	1156
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	120.0 Å
Rg (实空间) rg_real	37.18 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	2.8200e+08
I(0) 误差 (实空间) i0_real_error	4.2710e+06
Rg (倒空间) rg_reciprocal	37.20 Å
I(0) (倒空间) i0_reciprocal	282000000.0000
解质量估计 total_estimate	0.8998
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	39.1 Å
偏度 Skewness skewness	0.262
峰度 Kurtosis kurtosis	-0.650
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	89230000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.955

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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	heat shock-like protein 1
分子量 formula_weight	39074.2 kDa
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	B,A,C,D
原子数 atom_count	10108

GPLGSMADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

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	4

Entity 3 non-polymer

描述 description	N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE
分子量 formula_weight	378.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
分子量 formula_weight	458.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	419

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1xmma1
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	d1xmma2
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	d1xmmb1
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	d1xmmb2
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	d1xmmc1
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	d1xmmc2
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	d1xmmd1
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	d1xmmd2
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 (10 domains)

结构域编号 domain_id	1xmmA01
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	1xmmA02
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	1xmmB01
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	1xmmB02
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	1xmmB03
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	1xmmC01
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	1xmmC02
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	1xmmC03
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	1xmmD01
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	1xmmD02
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	100.928 Å
晶胞边长 b length_b	105.140 Å
晶胞边长 c length_c	138.647 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	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2162
R_work r_work	0.2135
R_free r_free	0.2670

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