8i24

Clostridium thermocellum RNA polymerase transcription open complex with SigI6 and its promoter

Method: ELECTRON MICROSCOPY D_max: 161.2 Å Quality: GOOD

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	8i24
沉积日期 deposition_date	2023-01-13
结构标题 title	Clostridium thermocellum RNA polymerase transcription open complex with SigI6 and its promoter
关键词 keywords	TRANSCRIPTION OPEN COMPLEX, SIGI, TRANSCRIPTION; TRANSCRIPTION
实验方法 method	ELECTRON MICROSCOPY

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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	49.24 Å
回转半径 Rg (电子) rg_electron	48.18 Å
零角强度 I(0) i0	2243790000.00
分子量 molecular_weight	376250.0 kDa
排除体积 excluded_volume	463800 Å³
包络体积 envelope_volume	662250 Å³
水化壳体积 shell_volume	110130 Å³
包络直径 envelope_diameter	170.2 Å
壳层 Rg shell_rg	55.37 Å
包络 Rg envelope_rg	47.74 Å
形状 Rg shape_rg	48.14 Å
总 Rg total_rg	48.52 Å
总原子数 total_atoms	26321
残基数 n_residues	3178
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	161.2 Å
Rg (实空间) rg_real	49.02 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	2.2440e+09
I(0) 误差 (实空间) i0_real_error	3.7230e+07
Rg (倒空间) rg_reciprocal	49.24 Å
I(0) (倒空间) i0_reciprocal	2244000000.0000
解质量估计 total_estimate	0.8714
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	60.5 Å
偏度 Skewness skewness	0.266
峰度 Kurtosis kurtosis	-0.305
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	429500000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.810

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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 (9)

Entity 1 polymer

描述 description	DNA-directed RNA polymerase subunit alpha
分子量 formula_weight	35071.1 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,A
原子数 atom_count	26321

MIEIEKPKIECVVCSEDNRYGKFVVEPLERGYGITLGNSLRRILLSSLPGVAVTSIKIDGVLHEFSTIPGVIEDVTEIILNIKELSLNFHGEGPKVIYIDAEGEGEVKAKDIKADADVEILNPEHKIATLSGDHRLYMEMTIDKGRGYVSAEKNKHPGQPIGVIPVDSIFTPVHKVNYTVENTRVGQVTDYDKLTLEVWTNGSIKPDEAISLGAKILSEHLNLFIDLSDNAKNAEIMVEKEETKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEDLISRTEEDMMKVRNLGRKSLEEVVNKLKALGLSLAPSED

Entity 2 polymer

描述 description	DNA-directed RNA polymerase subunit beta
分子量 formula_weight	140110.4 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

MVHPVKLGRNVRMSYSKIDEVIDMPNLIEIQKNSYEQFLKEGFKEVFKDVNPITDYTGNLILEFVDYSLDEPPKYSVDECKERDATYAAPLKVKVRLINKETGEVKEQEIFMGDFPLMTETGTFIINGAERVIVSQLVRSPGIYYAMKIDKAGKQLFSNTVIPNRGAWLEYETDSNDVLSVRIDRTRKLPLTVLVRALGYGTDLEITELFGEDERILATIQKDSTKTEEEGLLEIYKRLRPGEPPTVESAKALLHGLFFDPKRYDLAKPGRFKFNKKLSIAARIHGFIAGENIKDPDTGEIIVAEGETISREKAETIQNAGVNTVILRVDGKNVKVIGNDMVDIKRYVDFDPKEIGINEKVKRDVLMEILEEYKGKGDDAIKKALQERIDDLIPKHITKEDIISSISYIIGLSYGIGSTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMTIQDLDVVTPQALINIRPVAAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLIGSLSTYARVNEYGFIETPYRKVSKEEPGKVTNEIVYLTADEEDEYIIAQANEPLDEEGRFISNKVVCRYKEEFIEVDPSKIDFMDVSPKQIVSVATSMIPFLENDDANRALMGANMQRQAVPLIKTESPIVGTGIEYRAARDSGVVILAKNPGVVEKVTANEIIIRTKDGKRDTYKLLKYMRSNQGTCINQRPIVKKGEEVEAGDVIADGPSTDNGEIALGKNVLVGFMTWEGYNYEDAILISERLVKDDVFTSIHIEEYEAEARDTKLGPEDITREIPNVSEDALKDLNSEGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGESGIVVDVKIFTRENGDELAPGVNKLVRVYVAQKRKISVGDKMAGRHGNKGVISRILPVEDMPFLPDGTPLDIVLNPLGVPSRMNIGQVLEVHLGYAAKALGWKVATPVFDGATEEDIVQTLRKAGLAEDGKSILYDGRTGEPFENRVTVGYMYMLKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGENVPEPGIPESFKVLIKELQSLCLDVKVYSEEQEEIAIKESVEDDLEELNVNIEGREDEVNFNEFNDIGEEITDEDLEVEDFDLQDLNDDDINPDDTIDAELDDNLFDDDFDDTFDDDDL

Entity 3 polymer

描述 description	;DNA-directed RNA polymerase subunit beta' ;
分子量 formula_weight	132698.8 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

MGSSHHHHHHHHHHSGSGSGSGSGFELNNFDSIRIGLASPEKIREWSRGEVKKPETINYRTLKPERDGLFCERIFGPQKDWECHCGKYKRIRYKGIVCDRCGVEVTRSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEKILYFAAYVVIDPGQTPLSKKQILSEKEYRDSLEKFGPKFRAGMGAEAVRELLQEINLDELSAELREEIKQSTGQKRVRAIKRLEVVEAFRQSQNKPEWMILDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPDIIVRNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKIYQCGLPKEMALELFKPFVMKKLVNDGLAHNIKSAKRMVERVRNEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGRALKLHPLVCTAYNADFDGDQMAIHVPLSAEAQAEARFLMLSANNLLKPQDGKPVAVPTQDMVLGSYYLTILKEGAKGEGRVFTSMDEAVMAYDNGEIELHSKIKVRMKRVVDGVEKSKIIETTLGRLIFNEAIPQDLGFVDRSDPDKIFDLEVDFLVGKNELKKIIDKSIKVHGTTKTAILLDKIKELGFKYSTKGAITISISDMVIPEVKAKYIKETEEKIEKITKQYKRGLISDEERYNSVIAAWTEASENITRALINNLDRFNPVYMMSQSGARGNINQIKQLAGMRGLMADTSGKTIEFPIKANFREGLTVMEFFISTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVRETDCGTRKGIEVTDIKDGNEVIEELSERIIGRYPVGNIVHPETGEIIVEAGRMITDQDAEKIVKAGIKKVRIRSVLTCHSEYGVCAKCYGANLATGEECNVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGEDITQGLPRVEELFEARKPKGLAIISEIKGTVKISETKKKREIVVTSEDGETRSYLIPYGSRIKVSDGDQVEAGDELTEGSVNPHDILKIKGVEAVQTYLVHEVQKVYRMQGVDINDKHIEVIVRQMLRKVKVEDPGDTSLLPGGLVDVFDFEEENAKAIAEGKKPAVAKRALLGITKAALATDSFLSAASFQETTRVLTEAAIKGKVDPLVGLKENVIIGKLIPAGTGMSRYKDITISTVTE

Entity 4 polymer

描述 description	DNA-directed RNA polymerase subunit omega
分子量 formula_weight	8783.1 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E

MKEKKERVSSMIEPSINSLLEKVDSRYTLVVATAKRARQLTDGANKLTNCESDKPVTVAINEINENKITYIRTKSGIK

Entity 5 polymer

描述 description	RNA polymerase sigma factor SigI6
分子量 formula_weight	30092.4 kDa
突变 mutation	C167S
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F

SMDWHFQGTNDDREHTKRIIIEYLNRIKAGDDSAREEFILRFRPFILKLVYKATDRHVEPENSEEYSVALLAFNEAINAYDEEKHSNFLVFSEQVINRRLIDYKRKNHKNKMVYPFSYFENEDIKLERTLSDADGNNAIERLEFTDEIRLFKSELASFDITFKDLLSSTPKHRDSRELLINIAKKIASNDGLYEKLKKTKKLPTLELLKLAKVSRRTIERNKKYIIAVSLILRSNLEIFKEYAAGIQEKEVDLR

来源 Source

来源生物 organism	Acetivibrio thermocellus DSM 1313
NCBI 分类编号 ncbi_taxonomy_id	637887
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

描述 description	DNA (80-mer)
分子量 formula_weight	24795.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	O

GATCCACCTGGGAAGCTGACAATGCGACATAAAACCATTCCGGTATACGAATCGATATAAGAATAAGGGGTGAAATTAAC

Entity 7 polymer

描述 description	DNA (80-mer)
分子量 formula_weight	24606.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	P

GTTAATTTCACCCCTTATAGAATATAGCATTCGTATACCGGAATGGTTTTATGTCGCATTGTCAGCTTCCCAGGTGGATC

Entity 8 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

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

分辨率 resolution	3.36 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	22500

fit	/app/data/saxs_computation/i2/8i24/8i24.fit
pddf	/app/data/pr_computation/i2/8i24/8i24.pr.out
profile	/app/data/saxs_computation/i2/8i24/8i24.dat

Clostridium thermocellum RNA polymerase transcription open complex with SigI6 and its promoter

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (9)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 non-polymer

Entity 9 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)