8dy9

Streptomyces venezuelae RNAP unconstrained open promoter complex with WhiA and WhiB transcription factors

Method: ELECTRON MICROSCOPY D_max: 199.0 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	8dy9
沉积日期 deposition_date	2022-08-03
结构标题 title	Streptomyces venezuelae RNAP unconstrained open promoter complex with WhiA and WhiB transcription factors
关键词 keywords	RNA polymerase, Transcription factor, Iron cluster, TRANSCRIPTION-TRANSFERASE-DNA complex; TRANSCRIPTION/TRANSFERASE/DNA
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	56.46 Å
回转半径 Rg (电子) rg_electron	54.95 Å
零角强度 I(0) i0	3521590000.00
分子量 molecular_weight	462410.0 kDa
排除体积 excluded_volume	564950 Å³
包络体积 envelope_volume	870800 Å³
水化壳体积 shell_volume	128540 Å³
包络直径 envelope_diameter	217.7 Å
壳层 Rg shell_rg	59.93 Å
包络 Rg envelope_rg	54.91 Å
形状 Rg shape_rg	54.90 Å
总 Rg total_rg	55.22 Å
总原子数 total_atoms	63435
残基数 n_residues	3921
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	199.0 Å
Rg (实空间) rg_real	56.42 Å
Rg 误差 (实空间) rg_real_error	2.05 Å
I(0) (实空间) i0_real	3.5220e+09
I(0) 误差 (实空间) i0_real_error	7.8790e+07
Rg (倒空间) rg_reciprocal	56.48 Å
I(0) (倒空间) i0_reciprocal	3522000000.0000
解质量估计 total_estimate	0.8541
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	64.0 Å
偏度 Skewness skewness	0.385
峰度 Kurtosis kurtosis	-0.131
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	437000000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.733; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.904

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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)

Entity 1 polymer

描述 description	DNA-directed RNA polymerase subunit alpha
分子量 formula_weight	36734.6 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	63435

MLIAQRPSLTEEVVDEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNPDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTDAALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKLAGMGLALKDSPPGFDPTAAADAFGADDDADAGFVETEQY

来源 Source

来源生物 organism	Streptomyces venezuelae ATCC 10712
NCBI 分类编号 ncbi_taxonomy_id	953739
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	DNA-directed RNA polymerase subunit beta
分子量 formula_weight	130459.0 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

MQGTGTRVVSPSPRKDPLLAASRNASTNTNNGASTAPLRISFAKIKEPLEVPNLLALQTESFDWLLGNAAWKARVEAALESGQDVPTKSGLEEIFEEISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYGAPLFVTAEFTNNETGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKTSDKDIFSAKIIPSRGAWLEMEIDKRDLVGVRIDRKRKQSVTVLLKALGWTTEQILQEFGEYESMRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETIGENGNEIVVETDDIDHFGNRRLRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRVNAFGFIETPYRKVVDGQVTDEVDYVTADEEDRFVIAQANAALDEELRFSENRVLVRKRGGEVDYVEPSDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAVPLIKSEAPLVGTGMEYRCATDAGDVLKAEKDGVVQELSADYITVANDDGTYITYRLHKFSRSNQGTSVNQKVVVDEGDRVIEGQVLADGPATEDGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKIIGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKILPIEDMPFLEDGTPVDIILNPLGVPSRMNPGQVLEIHLGWLASRGWDVSGLADEWAQRLQAIGADKVAPGTNVATPVFDGAREDELAGLLNHTIPNRDGERMVLPTGKARLFDGRSGEPFPDPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDEDVFRAAEELGIDLSRREPSSVEEV

Entity 3 polymer

描述 description	;DNA-directed RNA polymerase subunit beta' ;
分子量 formula_weight	144614.8 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

DDVNFFDELRIGLATADDIRQWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITYVDDERRTRDLPSLEAHVSVERQQIENRRDSDLEARAKKLENDLGELEAEGAKADVRRKVREGAEREMKQLRDRAQREIDRLDEVWSRFKNLKVQDLEGDELLYRELRDRFGTYFDGSMGAAALQKRLESFDLEEEAERLREIIRTGKGQKKTRALKRLKVVSAFLQTANSPKGMVLDCVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDALFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSARSVIVVGPQLKLHQCGLPKAMALELFKPFVMKRLVDLNHAQNIKSAKRMVERGRTVVYDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPQLVEGKAIQIHPLVCTAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILKPADGRPVTMPTQDMVLGLFFLTTDGELRDTKGEGRAFGSTAEAIMAFDAGELALQSQIDIRFPVGTVAPRGWVPPVTEEGEPEWQQGDSFRLRTSLGRALFNELLPEDYPFVDYSVGKKQLSEIVNDLAERYPKVIVAATLDNLKAAGFYWATRSGVTVAISDVVVPEAKKAIVKGYEEQDEKVQKQYERGLITKEERTQELIAIWTKATNEVAEAMNANFPKTNPIFMMVDSGARGNMMQMRQIAGMRGLVSNAKNETIPRPIKASFREGLTVLEYFISTHGARKGLADTALRTADSGYLTRRLVDVSQDVIIREEDCGTERGLKLRIAERGADGVLRKTDDVETSVYARMLAEDVVVDGKVIAPANVDLGDVLIDALVGAGVEEVKTRSVLTCESAVGTCAFCYGRSLATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRVVELFEARQPKGVAPISEAAGRVRIEETEKTKKIVVTPDDGTDETAFPISKRARLLVGEGDHVEVGQKLTVGATNPHDVLRILGQRAVQVHLVAEVQKVYNSQGVSIHDKHIEIIIRQMLRRVTIIESGDAELLPGELVERSKFETENRRVVTEGGHPASGRPQLMGITKASLATESWLSAASFQETTRVLTDAAINAKSDSLIGLKENVIIGKLIPAGTGLSRYRNIRVEPTEEAKAAMYSAVGYDDIDYSPFGSGSGQAVPLEDYDYGPYNQ

Entity 4 polymer

描述 description	DNA-directed RNA polymerase subunit omega
分子量 formula_weight	9731.0 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

MSSSITAPEGIINPPIDELLEATDSKYSLVIYAAKRARQINAYYSQLGEGLLEYVGPLVDTHVHEKPLSIALREINAGLLTSEAIEGPAQ

Entity 5 polymer

描述 description	RNA polymerase sigma factor SigA
分子量 formula_weight	56696.2 kDa
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

FVSASTSRTLPPEIAESESVMALIERGKADGQIAGDDVRRAFEADQIPPTQWKNVLRSLNQILEEEGVTLMVSAAESPKRARKSVAAKSPAKRTATKTVTARTTVTKTTVTAAPASAAEDADPADEAGSAAKKTAAKKTVAKKTVAKKTVAKKTAAKKTTSKKDADELVEGEELLEDVAPGKGEEEETEGESKGFVLSDEDEDDAPAQQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD

来源 Source

来源生物 organism	Streptomyces venezuelae
NCBI 分类编号 ncbi_taxonomy_id	54571
宿主生物 host_organism	Escherichia coli

Entity 6 polymer

描述 description	RNA polymerase-binding protein RbpA
分子量 formula_weight	14116.1 kDa
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	G

MSERALRGTRLVVTSYETDRGIDLAPRQAVEYACEKGHRFEMPFSVEAEIPPEWECKVCGIQALLVDGDGPEEKKGKPARTHWDMLMERRTREELEEVLAERLAVLRSGAMNIAVHPRDSRKSA

来源 Source

来源生物 organism	Streptomyces venezuelae
NCBI 分类编号 ncbi_taxonomy_id	54571
宿主生物 host_organism	Escherichia coli

Entity 7 polymer

描述 description	Transcriptional regulator WhiB
分子量 formula_weight	10011.2 kDa
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	H

MTELFQELLVEDADEELGWQERALCAQTDPESFFPEKGGSTREAKKVCLACEVRSECLEYALQNDERFGIWGGLSERERRRLKKAAV

来源 Source

来源生物 organism	Streptomyces venezuelae
NCBI 分类编号 ncbi_taxonomy_id	54571
宿主生物 host_organism	Escherichia coli

Entity 8 polymer

描述 description	Probable cell division protein WhiA
分子量 formula_weight	34959.2 kDa
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	I

MTAAVKDEISRLPVTRTCCRKAEVSSILRFAGGLHLVSGRIVIEAELDTAMAARRLKRDILEIFGHSSELIVMAPGGLRRGSRFVVRVVAGGDQLARQTGLVDGRGRPIRGLPPQVVSGATCDAEAAWRGAFLAHGSLTEPGRSSSLEVTCPGPEAALALVGAARRLSIAAKAREVRGVDRVVVRDGDAIGALLTRLGAHESVLAWEERRMRREVRATANRLANFDDANLRRSARAAVAAGARVQRALEILGEEVPEHLAAAGRLRMEHKQASLEELGALADPPLTKDAVAGRIRRLLAMADKRAQDLGIPGTESNLTEELDDSLVG

来源 Source

来源生物 organism	Streptomyces venezuelae
NCBI 分类编号 ncbi_taxonomy_id	54571
宿主生物 host_organism	Escherichia coli

Entity 9 polymer

描述 description	DNA (38-MER)
分子量 formula_weight	15068.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	O,Q

GTGATATCAGCCAGATCGTGCGACACACCGGGCCAATTGGCTTGACACC

Entity 10 polymer

描述 description	DNA (38-MER)
分子量 formula_weight	15121.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	P,R

GGTGTCAAGCCAATTGGCCCGGTGTGTCGCACGATCTGGCTGATATCAC

Entity 11 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	3

Entity 12 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

Entity 13 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

结构域编号 domain_id	8dy9A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

结构域编号 domain_id	8dy9B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

结构域编号 domain_id	8dy9D01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

结构域编号 domain_id	8dy9D02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	132 — Topoisomerase I; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	30 — RNA polymerase Rpb1 funnel domain

结构域编号 domain_id	8dy9I01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	28 — Endonuclease I-creI
同源超家族 H-superfamily homologous superfamily	10 — Homing endonucleases

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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	3.12 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	118181

fit	/app/data/saxs_computation/dy/8dy9/8dy9.fit
pddf	/app/data/pr_computation/dy/8dy9/8dy9.pr.out
profile	/app/data/saxs_computation/dy/8dy9/8dy9.dat

Streptomyces venezuelae RNAP unconstrained open promoter complex with WhiA and WhiB transcription factors

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 (13)

Entity 1 polymer

聚合体 Polymer

来源 Source

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

来源 Source

Entity 7 polymer

聚合体 Polymer

来源 Source

Entity 8 polymer

聚合体 Polymer

来源 Source

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

6. 折叠分类 (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)