1loj

;Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP) ;

Method: X-RAY DIFFRACTION D_max: 90.1 Å Quality: EXCELLENT

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	1loj
沉积日期 deposition_date	2002-05-06
结构标题 title	;Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP) ;
关键词 keywords	beta barrel, OB-fold, heptameric toroid, tetradecamer, RNA BINDING PROTEIN, transcription; RNA BINDING PROTEIN, transcription
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	31.07 Å
回转半径 Rg (电子) rg_electron	29.87 Å
零角强度 I(0) i0	239895000.00
分子量 molecular_weight	122290.0 kDa
排除体积 excluded_volume	153290 Å³
包络体积 envelope_volume	192100 Å³
水化壳体积 shell_volume	50459 Å³
包络直径 envelope_diameter	100.3 Å
壳层 Rg shell_rg	39.25 Å
包络 Rg envelope_rg	29.75 Å
形状 Rg shape_rg	29.88 Å
总 Rg total_rg	30.65 Å
总原子数 total_atoms	8587
残基数 n_residues	1047
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	90.1 Å
Rg (实空间) rg_real	30.80 Å
Rg 误差 (实空间) rg_real_error	0.38 Å
I(0) (实空间) i0_real	2.3990e+08
I(0) 误差 (实空间) i0_real_error	3.3980e+06
Rg (倒空间) rg_reciprocal	30.92 Å
I(0) (倒空间) i0_reciprocal	239900000.0000
解质量估计 total_estimate	0.9021
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	42.4 Å
偏度 Skewness skewness	0.044
峰度 Kurtosis kurtosis	-0.496
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	393000000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.922

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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 (6)

Entity 1 polymer

描述 description	small nuclear ribonucleoprotein homolog (Sm-like)
分子量 formula_weight	9645.1 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
原子数 atom_count	8974

MIDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGKLAAA

来源 Source

来源生物 organism	Methanothermobacter thermautotrophicus str. Delta H
NCBI 分类编号 ncbi_taxonomy_id	187420
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	5

Entity 3 non-polymer

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	14

Entity 4 non-polymer

描述 description	URIDINE
分子量 formula_weight	244.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 5 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	1

Entity 6 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	387

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6. 折叠分类 (SCOP + CATH) 42 domains

SCOP 2.08 (28 domains)

结构域编号 domain_id	d1loja1
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	d1loja2
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	d1lojb1
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	d1lojb2
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	d1lojc1
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	d1lojc2
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	d1lojd1
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	d1lojd2
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	d1loje1
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	d1loje2
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	d1lojf1
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	d1lojf2
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	d1lojg1
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	d1lojg2
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	d1lojh1
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	d1lojh2
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	d1loji1
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	d1loji2
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	d1lojj1
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	d1lojj2
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	d1lojk1
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	d1lojk2
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	d1lojl1
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	d1lojl2
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	d1lojm1
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	d1lojm2
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	d1lojn1
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	d1lojn2
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

CATH v4.4 (14 domains)

结构域编号 domain_id	1lojA00
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	1lojB00
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	1lojC00
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	1lojD00
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	1lojE00
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	1lojF00
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	1lojG00
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	1lojH00
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	1lojI00
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	1lojJ00
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	1lojK00
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	1lojL00
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	1lojM00
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	1lojN00
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 (2)

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晶胞边长 a length_a	65.254 Å
晶胞边长 b length_b	109.956 Å
晶胞边长 c length_c	83.756 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.81 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	28

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	19.790 Å
R 因子 r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2500