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Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui

Method: X-RAY DIFFRACTION Dmax: 265.0 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1yit

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id1yit
沉积日期 deposition_date2005-01-13
结构标题 titleCrystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui
关键词 keywords;VIRGINIAMYCIN M, VIRGINIAMYCIN S, PEPTIDYL TRANSFERASE, RIBOSOME, STREPTOGRAMIN, RIBOSOME-ANTIBIOTIC COMPLEX, ANTIBIOTIC, CYCLOHEXADEPSIPEPTIDE ;; RIBOSOME/ANTIBIOTIC
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_guinier69.03 Å
回转半径 Rg (电子) rg_electron69.42 Å
零角强度 I(0) i085702600000.00
分子量 molecular_weight1292400.0 kDa
排除体积 excluded_volume1056800 ų
包络体积 envelope_volume2190100 ų
水化壳体积 shell_volume241430 ų
包络直径 envelope_diameter238.8 Å
壳层 Rg shell_rg81.61 Å
包络 Rg envelope_rg69.44 Å
形状 Rg shape_rg69.63 Å
总 Rg total_rg69.22 Å
总原子数 total_atoms91326
残基数 n_residues6648
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 dmax265.0 Å
Rg (实空间) rg_real72.73 Å
Rg 误差 (实空间) rg_real_error1.61 Å
I(0) (实空间) i0_real8.6160e+10
I(0) 误差 (实空间) i0_real_error1.6720e+09
Rg (倒空间) rg_reciprocal69.63 Å
I(0) (倒空间) i0_reciprocal85830000000.0000
解质量估计 total_estimate0.8657
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary92.2 Å
偏度 Skewness skewness0.633
峰度 Kurtosis kurtosis0.633
角度范围 angular_range— – 0.1150 Å−1
当前正则化参数 α current_alpha0.8618
最高正则化参数 α highest_alpha7144000000.0000
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: 0.587; Stabil: 0.869; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.909
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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 (38)

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6. 折叠分类 (SCOP + CATH) 67 domains

SCOP 2.08 (31 domains)

结构域编号 domain_idd1yit11
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.8 — Zn-binding ribosomal proteins
家族 Family familyg.41.8.2 — Ribosomal protein L37e
结构域编号 domain_idd1yit21
类 Class classa — All alpha proteins
折叠类型 Fold folda.137 — Non-globular all-alpha subunits of globular proteins
超家族 Superfamily superfamilya.137.1 — Ribosomal protein L39e
家族 Family familya.137.1.1 — Ribosomal protein L39e
结构域编号 domain_idd1yit31
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.8 — Zn-binding ribosomal proteins
家族 Family familyg.41.8.3 — Ribosomal protein L44e
结构域编号 domain_idd1yita1
类 Class classb — All beta proteins
折叠类型 Fold foldb.34 — SH3-like barrel
超家族 Superfamily superfamilyb.34.5 — Translation proteins SH3-like domain
家族 Family familyb.34.5.3 — C-terminal domain of ribosomal protein L2
结构域编号 domain_idd1yita2
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_idd1yitb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamilyb.43.3 — Translation proteins
家族 Family familyb.43.3.2 — Ribosomal protein L3
结构域编号 domain_idd1yitc1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.22 — Ribosomal protein L4
超家族 Superfamily superfamilyc.22.1 — Ribosomal protein L4
家族 Family familyc.22.1.1 — Ribosomal protein L4
结构域编号 domain_idd1yitd1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.77 — RL5-like
超家族 Superfamily superfamilyd.77.1 — RL5-like
家族 Family familyd.77.1.1 — Ribosomal protein L5
结构域编号 domain_idd1yite1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.141 — Ribosomal protein L6
超家族 Superfamily superfamilyd.141.1 — Ribosomal protein L6
家族 Family familyd.141.1.1 — Ribosomal protein L6
结构域编号 domain_idd1yite2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.141 — Ribosomal protein L6
超家族 Superfamily superfamilyd.141.1 — Ribosomal protein L6
家族 Family familyd.141.1.1 — Ribosomal protein L6
结构域编号 domain_idd1yitf1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.79 — Bacillus chorismate mutase-like
超家族 Superfamily superfamilyd.79.3 — L30e-like
家族 Family familyd.79.3.1 — L30e/L7ae ribosomal proteins
结构域编号 domain_idd1yitg1
类 Class classj — Peptides
折叠类型 Fold foldj.84 — Ribosomal protein L10
超家族 Superfamily superfamilyj.84.1 — Ribosomal protein L10
家族 Family familyj.84.1.1 — Ribosomal protein L10
结构域编号 domain_idd1yith1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.41 — alpha/beta-Hammerhead
超家族 Superfamily superfamilyd.41.4 — Ribosomal protein L16p/L10e
家族 Family familyd.41.4.1 — Ribosomal protein L10e
结构域编号 domain_idd1yiti1
类 Class classa — All alpha proteins
折叠类型 Fold folda.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamilya.4.7 — Ribosomal protein L11, C-terminal domain
家族 Family familya.4.7.1 — Ribosomal protein L11, C-terminal domain
结构域编号 domain_idd1yitj1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.21 — Ribosomal protein L13
超家族 Superfamily superfamilyc.21.1 — Ribosomal protein L13
家族 Family familyc.21.1.1 — Ribosomal protein L13
结构域编号 domain_idd1yitk1
类 Class classb — All beta proteins
折叠类型 Fold foldb.39 — Ribosomal protein L14
超家族 Superfamily superfamilyb.39.1 — Ribosomal protein L14
家族 Family familyb.39.1.1 — Ribosomal protein L14
结构域编号 domain_idd1yitl1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.12 — Ribosomal proteins L15p and L18e
超家族 Superfamily superfamilyc.12.1 — Ribosomal proteins L15p and L18e
家族 Family familyc.12.1.1 — Ribosomal proteins L15p and L18e
结构域编号 domain_idd1yitm1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.12 — Ribosomal proteins S24e, L23 and L15e
超家族 Superfamily superfamilyd.12.1 — Ribosomal proteins S24e, L23 and L15e
家族 Family familyd.12.1.2 — L15e
结构域编号 domain_idd1yitn1
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_idd1yito1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.12 — Ribosomal proteins L15p and L18e
超家族 Superfamily superfamilyc.12.1 — Ribosomal proteins L15p and L18e
家族 Family familyc.12.1.1 — Ribosomal proteins L15p and L18e
结构域编号 domain_idd1yitp1
类 Class classa — All alpha proteins
折叠类型 Fold folda.94 — Ribosomal protein L19 (L19e)
超家族 Superfamily superfamilya.94.1 — Ribosomal protein L19 (L19e)
家族 Family familya.94.1.1 — Ribosomal protein L19 (L19e)
结构域编号 domain_idd1yitq1
类 Class classb — All beta proteins
折叠类型 Fold foldb.34 — SH3-like barrel
超家族 Superfamily superfamilyb.34.5 — Translation proteins SH3-like domain
家族 Family familyb.34.5.1 — Ribosomal proteins L24p and L21e
结构域编号 domain_idd1yitr1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.55 — Ribosomal protein L22
超家族 Superfamily superfamilyd.55.1 — Ribosomal protein L22
家族 Family familyd.55.1.1 — Ribosomal protein L22
结构域编号 domain_idd1yits1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.12 — Ribosomal proteins S24e, L23 and L15e
超家族 Superfamily superfamilyd.12.1 — Ribosomal proteins S24e, L23 and L15e
家族 Family familyd.12.1.1 — L23p
结构域编号 domain_idd1yitt1
类 Class classb — All beta proteins
折叠类型 Fold foldb.34 — SH3-like barrel
超家族 Superfamily superfamilyb.34.5 — Translation proteins SH3-like domain
家族 Family familyb.34.5.1 — Ribosomal proteins L24p and L21e
结构域编号 domain_idd1yitu1
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.39.1.6 — Ribosomal protein L24e
结构域编号 domain_idd1yitv1
类 Class classa — All alpha proteins
折叠类型 Fold folda.2 — Long alpha-hairpin
超家族 Superfamily superfamilya.2.2 — Ribosomal protein L29 (L29p)
家族 Family familya.2.2.1 — Ribosomal protein L29 (L29p)
结构域编号 domain_idd1yitw1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.59 — Ribosomal protein L30p/L7e
超家族 Superfamily superfamilyd.59.1 — Ribosomal protein L30p/L7e
家族 Family familyd.59.1.1 — Ribosomal protein L30p/L7e
结构域编号 domain_idd1yitx1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.29 — Ribosomal protein L31e
超家族 Superfamily superfamilyd.29.1 — Ribosomal protein L31e
家族 Family familyd.29.1.1 — Ribosomal protein L31e
结构域编号 domain_idd1yity1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.9 — Barstar-like
超家族 Superfamily superfamilyc.9.2 — Ribosomal protein L32e
家族 Family familyc.9.2.1 — Ribosomal protein L32e
结构域编号 domain_idd1yitz1
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.8 — Zn-binding ribosomal proteins
家族 Family familyg.41.8.1 — Ribosomal protein L37ae

CATH v4.4 (36 domains)

结构域编号 domain_id1yit100
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_id1yit200
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_id1yit300
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_id1yitA01
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_id1yitA02
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_id1yitA03
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_id1yitB01
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_id1yitB02
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_id1yitB03
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_id1yitC00
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_id1yitD00
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_id1yitE01
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_id1yitE02
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_id1yitF00
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_id1yitH00
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_id1yitI00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily250 — Ribosomal protein L11/L12, C-terminal domain
结构域编号 domain_id1yitJ00
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_id1yitK00
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_id1yitL01
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_id1yitL02
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_id1yitM00
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_id1yitN00
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_id1yitO00
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_id1yitP01
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_id1yitP02
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_id1yitP03
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_id1yitQ00
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_id1yitR00
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_id1yitS00
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_id1yitT00
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_id1yitU00
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_id1yitV00
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_id1yitW01
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_id1yitW02
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_id1yitX00
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_id1yitZ00
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 —
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7. 引用文献 (1)

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8. 文件与曲线 (10)