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1xnq

Structure of an Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center

Method: X-RAY DIFFRACTION Dmax: 221.3 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1xnq

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1xnq
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1xnq
沉积日期 deposition_date2004-10-05
结构标题 titleStructure of an Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center
关键词 keywordsribosome, decoding, translation, inosine; RIBOSOME
实验方法 methodX-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_guinier65.29 Å
回转半径 Rg (电子) rg_electron65.84 Å
零角强度 I(0) i018557300000.00
分子量 molecular_weight771890.0 kDa
排除体积 excluded_volume808000 ų
包络体积 envelope_volume1282500 ų
水化壳体积 shell_volume160250 ų
包络直径 envelope_diameter243.0 Å
壳层 Rg shell_rg67.42 Å
包络 Rg envelope_rg65.26 Å
形状 Rg shape_rg65.84 Å
总 Rg total_rg65.86 Å
总原子数 total_atoms52076
残基数 n_residues3905
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 Å−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
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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax221.3 Å
Rg (实空间) rg_real65.51 Å
Rg 误差 (实空间) rg_real_error2.64 Å
I(0) (实空间) i0_real1.8560e+10
I(0) 误差 (实空间) i0_real_error4.0710e+08
Rg (倒空间) rg_reciprocal65.07 Å
I(0) (倒空间) i0_reciprocal18540000000.0000
解质量估计 total_estimate0.8456
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary73.8 Å
偏度 Skewness skewness0.438
峰度 Kurtosis kurtosis-0.266
角度范围 angular_range— – 0.1200 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha1318000000.0000
实空间数据点数 n_real_points25
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.474
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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 (26)

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6. 折叠分类 (SCOP + CATH) 47 domains

SCOP 2.08 (22 domains)

结构域编号 domain_idd1xnqb_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.23 — Flavodoxin-like
超家族 Superfamily superfamilyc.23.15 — Ribosomal protein S2
家族 Family familyc.23.15.1 — Ribosomal protein S2
结构域编号 domain_idd1xnqc1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.52 — Alpha-lytic protease prodomain-like
超家族 Superfamily superfamilyd.52.3 — Prokaryotic type KH domain (KH-domain type II)
家族 Family familyd.52.3.1 — Prokaryotic type KH domain (KH-domain type II)
结构域编号 domain_idd1xnqc2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.53 — Ribosomal protein S3 C-terminal domain
超家族 Superfamily superfamilyd.53.1 — Ribosomal protein S3 C-terminal domain
家族 Family familyd.53.1.1 — Ribosomal protein S3 C-terminal domain
结构域编号 domain_idd1xnqd_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.66 — Alpha-L RNA-binding motif
超家族 Superfamily superfamilyd.66.1 — Alpha-L RNA-binding motif
家族 Family familyd.66.1.2 — Ribosomal protein S4 (bacteria)
结构域编号 domain_idd1xnqe1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
家族 Family familyd.14.1.1 — Translational machinery components
结构域编号 domain_idd1xnqe2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.50 — dsRBD-like
超家族 Superfamily superfamilyd.50.1 — dsRNA-binding domain-like
家族 Family familyd.50.1.2 — Ribosomal S5 protein, N-terminal domain
结构域编号 domain_idd1xnqf_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.14 — Ribosomal protein S6
家族 Family familyd.58.14.1 — Ribosomal protein S6
结构域编号 domain_idd1xnqg_
类 Class classa — All alpha proteins
折叠类型 Fold folda.75 — Ribosomal protein S7
超家族 Superfamily superfamilya.75.1 — Ribosomal protein S7
家族 Family familya.75.1.1 — Ribosomal protein S7
结构域编号 domain_idd1xnqh_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.140 — Ribosomal protein S8
超家族 Superfamily superfamilyd.140.1 — Ribosomal protein S8
家族 Family familyd.140.1.1 — Ribosomal protein S8
结构域编号 domain_idd1xnqi_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
家族 Family familyd.14.1.1 — Translational machinery components
结构域编号 domain_idd1xnqj_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.58 — Ferredoxin-like
超家族 Superfamily superfamilyd.58.15 — Ribosomal protein S10
家族 Family familyd.58.15.1 — Ribosomal protein S10
结构域编号 domain_idd1xnqk_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.55 — Ribonuclease H-like motif
超家族 Superfamily superfamilyc.55.4 — Translational machinery components
家族 Family familyc.55.4.1 — Ribosomal protein L18 and S11
结构域编号 domain_idd1xnql_
类 Class classb — All beta proteins
折叠类型 Fold foldb.40 — OB-fold
超家族 Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
家族 Family familyb.40.4.5 — Cold shock DNA-binding domain-like
结构域编号 domain_idd1xnqm_
类 Class classa — All alpha proteins
折叠类型 Fold folda.156 — S13-like H2TH domain
超家族 Superfamily superfamilya.156.1 — S13-like H2TH domain
家族 Family familya.156.1.1 — Ribosomal protein S13
结构域编号 domain_idd1xnqn_
类 Class classg — Small proteins
折叠类型 Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
超家族 Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
家族 Family familyg.39.1.7 — Ribosomal protein S14
结构域编号 domain_idd1xnqo_
类 Class classa — All alpha proteins
折叠类型 Fold folda.16 — S15/NS1 RNA-binding domain
超家族 Superfamily superfamilya.16.1 — S15/NS1 RNA-binding domain
家族 Family familya.16.1.2 — Ribosomal protein S15
结构域编号 domain_idd1xnqp_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.27 — Ribosomal protein S16
超家族 Superfamily superfamilyd.27.1 — Ribosomal protein S16
家族 Family familyd.27.1.1 — Ribosomal protein S16
结构域编号 domain_idd1xnqq_
类 Class classb — All beta proteins
折叠类型 Fold foldb.40 — OB-fold
超家族 Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
家族 Family familyb.40.4.5 — Cold shock DNA-binding domain-like
结构域编号 domain_idd1xnqr_
类 Class classa — All alpha proteins
折叠类型 Fold folda.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamilya.4.8 — Ribosomal protein S18
家族 Family familya.4.8.1 — Ribosomal protein S18
结构域编号 domain_idd1xnqs_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.28 — Ribosomal protein S19
超家族 Superfamily superfamilyd.28.1 — Ribosomal protein S19
家族 Family familyd.28.1.1 — Ribosomal protein S19
结构域编号 domain_idd1xnqt_
类 Class classa — All alpha proteins
折叠类型 Fold folda.7 — Spectrin repeat-like
超家族 Superfamily superfamilya.7.6 — Ribosomal protein S20
家族 Family familya.7.6.1 — Ribosomal protein S20
结构域编号 domain_idd1xnqv_
类 Class classj — Peptides
折叠类型 Fold foldj.9 — Arg-rich RNA binding peptides
超家族 Superfamily superfamilyj.9.1 — 30S ribosomal protein THX
家族 Family familyj.9.1.1 — 30S ribosomal protein THX

CATH v4.4 (25 domains)

结构域编号 domain_id1xnqB01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10490 — Glucose-6-phosphate isomerase like protein; domain 1
结构域编号 domain_id1xnqB02
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 superfamily610 — Helix hairpin bin
结构域编号 domain_id1xnqC01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology300 — GMP Synthetase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily20 — K homology (KH) domain
结构域编号 domain_id1xnqC02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1140 — Ribosomal protein S3 C-terminal domain
同源超家族 H-superfamily homologous superfamily32 — Ribosomal protein S3, C-terminal domain
结构域编号 domain_id1xnqD01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1050 — Ribosomal Protein S4 Delta 41; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein S4/S9, N-terminal domain
结构域编号 domain_id1xnqD02
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
同源超家族 H-superfamily homologous superfamily10 — RNA-binding S4 domain
结构域编号 domain_id1xnqE01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily20 —
结构域编号 domain_id1xnqE02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id1xnqF00
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 superfamily60 — Ribosomal protein S6/Translation elongation factor EF1B
结构域编号 domain_id1xnqG00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology455 — Ribosomal Protein S7
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein S7/S5
结构域编号 domain_id1xnqH01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily30 —
结构域编号 domain_id1xnqH02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id1xnqI00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id1xnqJ00
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 superfamily600 — Ribosomal protein S10
结构域编号 domain_id1xnqK00
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 superfamily80 — Ribosomal protein S11/S14
结构域编号 domain_id1xnqL00
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_id1xnqM01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily50 —
结构域编号 domain_id1xnqM02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology910 — 30s ribosomal protein s13; domain 2
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein S13/S18, C-terminal domain
结构域编号 domain_id1xnqN00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology830 — 30s Ribosomal Protein S14; Chain N
同源超家族 H-superfamily homologous superfamily10 — Ribosomal Protein S14/S29
结构域编号 domain_id1xnqO00
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 superfamily10 — S15/NS1, RNA-binding
结构域编号 domain_id1xnqP00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1320 — S16 Ribosomal Protein; Chain: A;
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein S16
结构域编号 domain_id1xnqQ00
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_id1xnqR00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology640 — 30s Ribosomal Protein S18
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein S18
结构域编号 domain_id1xnqS00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology860 — 30s Ribosomal Protein S19; Chain A
同源超家族 H-superfamily homologous superfamily10 — Ribosomal protein S19/S15
结构域编号 domain_id1xnqT00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily110 — Ribosomal protein S20
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7. 引用文献 (1)

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8. 文件与曲线 (10)