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2b8k

12-subunit RNA Polymerase II

Method: X-RAY DIFFRACTION Dmax: 167.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 2b8k

P(r) 距离分布 P(r) Distribution

P(r) distribution for 2b8k
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id2b8k
沉积日期 deposition_date2005-10-07
结构标题 title12-subunit RNA Polymerase II
关键词 keywords;DNA-DIRECTED RNA POLYMERASE, DNA-DEPENDENT RNA POLYMERASE, CELLULAR RNA POLYMERASE, METAL-BINDING, NUCLEAR PROTEIN, TRANSCRIPTION, Transferase ;; TRANSFERASE
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_guinier51.53 Å
回转半径 Rg (电子) rg_electron50.98 Å
零角强度 I(0) i02801690000.00
分子量 molecular_weight442400.0 kDa
排除体积 excluded_volume553650 ų
包络体积 envelope_volume798240 ų
水化壳体积 shell_volume123460 ų
包络直径 envelope_diameter167.4 Å
壳层 Rg shell_rg59.68 Å
包络 Rg envelope_rg50.60 Å
形状 Rg shape_rg50.99 Å
总 Rg total_rg51.22 Å
总原子数 total_atoms31040
残基数 n_residues3925
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 dmax167.5 Å
Rg (实空间) rg_real51.33 Å
Rg 误差 (实空间) rg_real_error1.08 Å
I(0) (实空间) i0_real2.8020e+09
I(0) 误差 (实空间) i0_real_error5.4380e+07
Rg (倒空间) rg_reciprocal51.69 Å
I(0) (倒空间) i0_reciprocal2803000000.0000
解质量估计 total_estimate0.8796
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary64.8 Å
偏度 Skewness skewness0.176
峰度 Kurtosis kurtosis-0.414
角度范围 angular_range— – 0.1550 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha437400000.0000
实空间数据点数 n_real_points32
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.874
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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 (13)

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (16 domains)

结构域编号 domain_idd2b8ka1
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
超家族 Superfamily superfamilye.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
家族 Family familye.29.1.2 — RNA-polymerase beta-prime
结构域编号 domain_idd2b8kb1
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
超家族 Superfamily superfamilye.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
家族 Family familye.29.1.1 — RNA-polymerase beta
结构域编号 domain_idd2b8kc1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.74 — DCoH-like
超家族 Superfamily superfamilyd.74.3 — RBP11-like subunits of RNA polymerase
家族 Family familyd.74.3.1 — RNA polymerase alpha subunit dimerisation domain
结构域编号 domain_idd2b8kc2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.181 — Insert subdomain of RNA polymerase alpha subunit
超家族 Superfamily superfamilyd.181.1 — Insert subdomain of RNA polymerase alpha subunit
家族 Family familyd.181.1.1 — Insert subdomain of RNA polymerase alpha subunit
结构域编号 domain_idd2b8kd1
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd2b8ke1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.52 — Restriction endonuclease-like
超家族 Superfamily superfamilyc.52.3 — Eukaryotic RPB5 N-terminal domain
家族 Family familyc.52.3.1 — Eukaryotic RPB5 N-terminal domain
结构域编号 domain_idd2b8ke2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.78 — RPB5-like RNA polymerase subunit
超家族 Superfamily superfamilyd.78.1 — RPB5-like RNA polymerase subunit
家族 Family familyd.78.1.1 — RPB5
结构域编号 domain_idd2b8kf1
类 Class classa — All alpha proteins
折叠类型 Fold folda.143 — RPB6/omega subunit-like
超家族 Superfamily superfamilya.143.1 — RPB6/omega subunit-like
家族 Family familya.143.1.2 — RPB6
结构域编号 domain_idd2b8kg1
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_idd2b8kg2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.230 — Dodecin subunit-like
超家族 Superfamily superfamilyd.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
家族 Family familyd.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
结构域编号 domain_idd2b8kh1
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.40.4.8 — RNA polymerase subunit RBP8
结构域编号 domain_idd2b8ki1
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.3 — Zinc beta-ribbon
家族 Family familyg.41.3.1 — Transcriptional factor domain
结构域编号 domain_idd2b8ki2
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.3 — Zinc beta-ribbon
家族 Family familyg.41.3.1 — Transcriptional factor domain
结构域编号 domain_idd2b8kj1
类 Class classa — All alpha proteins
折叠类型 Fold folda.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamilya.4.11 — RNA polymerase subunit RPB10
家族 Family familya.4.11.1 — RNA polymerase subunit RPB10
结构域编号 domain_idd2b8kk1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.74 — DCoH-like
超家族 Superfamily superfamilyd.74.3 — RBP11-like subunits of RNA polymerase
家族 Family familyd.74.3.2 — RBP11/RpoL
结构域编号 domain_idd2b8kl1
类 Class classg — Small proteins
折叠类型 Fold foldg.41 — Rubredoxin-like
超家族 Superfamily superfamilyg.41.9 — RNA polymerase subunits
家族 Family familyg.41.9.2 — RBP12 subunit of RNA polymerase II
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7. 引用文献 (1)

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8. 文件与曲线 (10)