1m8v

Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer

Method: X-RAY DIFFRACTION D_max: 93.7 Å Quality: REASONABLE

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	1m8v
沉积日期 deposition_date	2002-07-26
结构标题 title	Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer
关键词 keywords	Protein-RNA complex, Sm protein, RNA BINDING PROTEIN-RNA COMPLEX; RNA BINDING PROTEIN/RNA
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	31.47 Å
回转半径 Rg (电子) rg_electron	31.01 Å
零角强度 I(0) i0	286274000.00
分子量 molecular_weight	129410.0 kDa
排除体积 excluded_volume	159730 Å³
包络体积 envelope_volume	200290 Å³
水化壳体积 shell_volume	51659 Å³
包络直径 envelope_diameter	99.1 Å
壳层 Rg shell_rg	39.93 Å
包络 Rg envelope_rg	30.53 Å
形状 Rg shape_rg	31.07 Å
总 Rg total_rg	31.55 Å
总原子数 total_atoms	9022
残基数 n_residues	1036
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	93.7 Å
Rg (实空间) rg_real	31.23 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	2.8630e+08
I(0) 误差 (实空间) i0_real_error	3.2560e+06
Rg (倒空间) rg_reciprocal	31.33 Å
I(0) (倒空间) i0_reciprocal	286300000.0000
解质量估计 total_estimate	0.6762
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.1 Å
偏度 Skewness skewness	0.115
峰度 Kurtosis kurtosis	-0.398
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	159500000.0000
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: 0.911; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.963; Smooth: 0.902

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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'-R(PUPUPUPUPUPUP*U)-3'
分子量 formula_weight	2098.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	O,P,Q,R,S,T,U
原子数 atom_count	9227

UUUUUUU

Entity 2 polymer

描述 description	PUTATIVE SNRNP SM-LIKE PROTEIN
分子量 formula_weight	8630.0 kDa
来源方法 src_method	man
拷贝数 entity_count	14

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N

GAMAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTEE

来源 Source

来源生物 organism	Pyrococcus abyssi
NCBI 分类编号 ncbi_taxonomy_id	29292
宿主生物 host_organism	Escherichia coli

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	7

Entity 4 non-polymer

描述 description	URIDINE-5'-MONOPHOSPHATE
分子量 formula_weight	324.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	14

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	205

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6. 折叠分类 (SCOP + CATH) 29 domains

SCOP 2.08 (15 domains)

结构域编号 domain_id	d1m8va1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8va2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1m8vb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8ve_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vf_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vg_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vh_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vi_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vj_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vk_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vl_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vm_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

结构域编号 domain_id	d1m8vn_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.38 — Sm-like fold
超家族 Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
家族 Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

CATH v4.4 (14 domains)

结构域编号 domain_id	1m8vA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vI00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vJ00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vK00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vL00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vM00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

结构域编号 domain_id	1m8vN00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	100 —

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7. 引用文献 (1)

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晶胞边长 a length_a	68.000 Å
晶胞边长 b length_b	68.000 Å
晶胞边长 c length_c	84.800 Å
晶胞夹角 α angle_alpha	105.00 °
晶胞夹角 β angle_beta	108.80 °
晶胞夹角 γ angle_gamma	100.00 °
晶胞分子数 Z z_pdb	14

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2120
R_free r_free	0.2820

fit	/app/data/saxs_computation/m8/1m8v/1m8v.fit
pddf	/app/data/pr_computation/m8/1m8v/1m8v.pr.out
profile	/app/data/saxs_computation/m8/1m8v/1m8v.dat

Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer

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

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 29 domains

SCOP 2.08 (15 domains)

CATH v4.4 (14 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)