1w2b

Trigger Factor ribosome binding domain in complex with 50S

Method: X-RAY DIFFRACTION Dmax: 262.9 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1w2b

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1w2b
下载 Download

1. 结构基本信息 1. Structure Basics

条目编号 entry_id1w2b
沉积日期 deposition_date2004-07-01
结构标题 titleTrigger Factor ribosome binding domain in complex with 50S
关键词 keywordsRIBOSOME, RIBOSOME_ASSOCIATED FACTORS, CHAPERONE, NASCENT CHAIN, COTRANSLATIONAL FOLDING, RNA-BINDING, RIBOSOMAL PROTEIN; RIBOSOME
实验方法 methodX-RAY DIFFRACTION

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier68.48
回转半径 Rg (电子) rg_electron69.24
零角强度 I(0) i060491800000.00
分子量 molecular_weight1353700.0 kDa
排除体积 excluded_volume1386100 ų
包络体积 envelope_volume2209300 ų
水化壳体积 shell_volume243530 ų
包络直径 envelope_diameter239.6
壳层 Rg shell_rg81.84
包络 Rg envelope_rg69.17
形状 Rg shape_rg69.33
总 Rg total_rg69.15
总原子数 total_atoms90972
残基数 n_residues6626
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax262.9
Rg (实空间) rg_real71.52
Rg 误差 (实空间) rg_real_error1.88
I(0) (实空间) i0_real6.0770e+10
I(0) 误差 (实空间) i0_real_error1.2870e+09
Rg (倒空间) rg_reciprocal69.08
I(0) (倒空间) i0_reciprocal60580000000.0000
解质量估计 total_estimate0.8570
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary91.4
偏度 Skewness skewness0.596
峰度 Kurtosis kurtosis0.595
角度范围 angular_range— – 0.1150 −1
当前正则化参数 α current_alpha0.7017
最高正则化参数 α highest_alpha7704000000.0000
实空间数据点数 n_real_points24
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.574; Stabil: 0.907; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.937

4. 晶体学与实验 4. Crystallography & Experiment

5. 实体与聚合体信息 (37)

6. 折叠分类 (SCOP + CATH) 63 domains

SCOP 2.08 (28 domains)

结构域编号 domain_idd1w2b1_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2b2_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2b5_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2ba_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bb_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bc_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bd_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2be_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bf_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bg_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bh_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bi_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bj_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bk_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bl_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bm_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bn_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bo_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bp_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2br_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bs_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bt_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bu_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bv_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bw_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bx_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2by_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit
结构域编号 domain_idd1w2bz_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.1 — Ribosome and ribosomal fragments
超家族 Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
家族 Family familyi.1.1.2 — Large subunit

CATH v4.4 (35 domains)

结构域编号 domain_id1w2b100
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1620 — Atp Synthase Epsilon Chain; Chain: I;
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L39
结构域编号 domain_id1w2b200
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily80
结构域编号 domain_id1w2bA01
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily30
结构域编号 domain_id1w2bA02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily140 — Nucleic acid-binding proteins
结构域编号 domain_id1w2bA03
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology950 — Ribosomal protein L2; domain 3
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L2, domain 3
结构域编号 domain_id1w2bB01
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily10 — Translation factors
结构域编号 domain_id1w2bB02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1430 — Ribosomal Protein L3; Chain: B; domain 2,
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1w2bB03
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology960 — Ribosomal protein L3; domain 3
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L3, domain 3
结构域编号 domain_id1w2bC00
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology1370 — Ribosomal Protein L4; Chain: A;
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L4/L1
结构域编号 domain_id1w2bD00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1440 — 50s Ribosomal Protein L5; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L5
结构域编号 domain_id1w2bE01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology930 — Outer Surface Protein A; domain 3
同源超家族 H-superfamily homologous superfamily12 — Ribosomal protein L6
结构域编号 domain_id1w2bE02
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology930 — Outer Surface Protein A; domain 3
同源超家族 H-superfamily homologous superfamily12 — Ribosomal protein L6
结构域编号 domain_id1w2bF00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
同源超家族 H-superfamily homologous superfamily30 — Ribosomal protein L30/S12
结构域编号 domain_id1w2bH00
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L16/L10
结构域编号 domain_id1w2bI00
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1180 — Ribosomal Protein L13p; Chain: A;
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L13
结构域编号 domain_id1w2bJ00
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology150 — Ribosomal Protein L14
同源超家族 H-superfamily homologous superfamily20 — Ribosomal protein L14/L23
结构域编号 domain_id1w2bK01
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology990 — Molecule: Ribosomal Protein L15; Chain: K; domain 1
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1w2bK02
类 Class class3 — Alpha Beta
架构 Architecture architecture100 — Ribosomal Protein L15; Chain: K; domain 2
拓扑 Topology topology10 — Ribosomal Protein L15; Chain: K; domain 2
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1w2bL00
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology1120 — Ribosomal protein L15e
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L15
结构域编号 domain_id1w2bM00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology420 — Nucleotidyltransferase; domain 5
同源超家族 H-superfamily homologous superfamily100
结构域编号 domain_id1w2bN00
类 Class class3 — Alpha Beta
架构 Architecture architecture100 — Ribosomal Protein L15; Chain: K; domain 2
拓扑 Topology topology10 — Ribosomal Protein L15; Chain: K; domain 2
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1w2bO01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1650 — 50s Ribosomal Protein L19e, Chain O, domain 1
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1w2bO02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
同源超家族 H-superfamily homologous superfamily60
结构域编号 domain_id1w2bO03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily560 — Single Heli x bin
结构域编号 domain_id1w2bP00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily70 — Ribosomal protein L21
结构域编号 domain_id1w2bQ00
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology470 — Ribosomal Protein L22; Chain A
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L22/L17
结构域编号 domain_id1w2bR00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
结构域编号 domain_id1w2bS00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily30
结构域编号 domain_id1w2bT00
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology170 — Ribosomal Protein L24e; Chain: T;
同源超家族 H-superfamily homologous superfamily20 — Ribosomal protein L24
结构域编号 domain_id1w2bU00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily310
结构域编号 domain_id1w2bV01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1390 — Ribosomal Protein L30; Chain: A,
同源超家族 H-superfamily homologous superfamily20 — Ribosomal protein L30/L7
结构域编号 domain_id1w2bV02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology15 — 3-methyladenine DNA Glycosylase II; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily30 — Ribosomal protein L30/L7, central domain
结构域编号 domain_id1w2bW00
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology440 — Ribosomal Protein L31e; Chain: W;
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein L31
结构域编号 domain_id1w2bY00
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily30
结构域编号 domain_id1w2bZ00
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily30

7. 引用文献 (1)

8. 文件与曲线 (10)