SAXSdb — 8dkc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8dkc
沉积日期 deposition_date	2022-07-05
结构标题 title	P. gingivalis RNA Polymerase
关键词 keywords	Porphyromonas gingivalis, RNA polymerase, transcription, CFB group bacteria; 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	49.92 Å
回转半径 Rg (电子) rg_electron	49.35 Å
零角强度 I(0) i0	1547680000.00
分子量 molecular_weight	330900.0 kDa
排除体积 excluded_volume	416150 Å³
包络体积 envelope_volume	620650 Å³
水化壳体积 shell_volume	102130 Å³
包络直径 envelope_diameter	171.4 Å
壳层 Rg shell_rg	55.77 Å
包络 Rg envelope_rg	48.48 Å
形状 Rg shape_rg	49.36 Å
总 Rg total_rg	49.56 Å
总原子数 total_atoms	23282
残基数 n_residues	2950
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	161.1 Å
Rg (实空间) rg_real	49.66 Å
Rg 误差 (实空间) rg_real_error	0.96 Å
I(0) (实空间) i0_real	1.5480e+09
I(0) 误差 (实空间) i0_real_error	2.7110e+07
Rg (倒空间) rg_reciprocal	49.91 Å
I(0) (倒空间) i0_reciprocal	1548000000.0000
解质量估计 total_estimate	0.6452
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	65.4 Å
偏度 Skewness skewness	0.236
峰度 Kurtosis kurtosis	-0.275
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	206100000.0000
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: 0.852; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.975; Smooth: 0.813

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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 (4)

Entity 1 polymer

描述 description	DNA-directed RNA polymerase subunit alpha
分子量 formula_weight	36838.1 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	23282

MAILAFQKPENVLMMETSDSIAKFEFKPLEPGYGITIGNALRRILLSSLEGFAITAIKIEGVEHEFATIPGVLEDVTNIILNLKQVRFKQIVPNADVEKATIVISNSEVFRAGDLNAQLSNFEVLNSNLVICHLDKSATLTMEFSINKGRGYVSAEENRAEHNELSTIAIDSIYTPIRNVKYAVENFRVEQKTDYEKLLMEVTTDGSIRPVDALREAAQILISHFSLFAENKIAIEYVDIVDTDEFDEDSLHMRQLLKSKLSGLDLSVRALNCLNAAGVDTLGDLVSLSRSDLMKIRNFGKKSLTELDELLATLNLSFGMDISKYKLDKD

来源 Source

来源生物 organism	Porphyromonas gingivalis
NCBI 分类编号 ncbi_taxonomy_id	837
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	142524.6 kDa
EC 编号 ec_number	2.7.7.6
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	C

MTPTTNNKRINFASIKNPLFYPDFLEVQLKSFHDFLQLDTPPERRKKEGLYKVFAENFPITDTRNNFVLEFLDYYIDPPKYSIEECLSRGLTYSVPLKAKLKLYCTDPDHEDFATVIQDVFLGPIPYMTSSGTFVINGAERVIVSQLHRSPGVFFGQSLHTNGTKLYSARIIPFKGSWIEFATDINNVMYAYIDRKKKLPVTTLLRAIGFEADKDILDIFNLADEVKVTKANLKKCIGRKLAARVINTYIDDLSDEDTGEVVSMERITVVVDREVELTEDNIEAILNSNAQTILLHRNDSNTSDYSIIFNTLQKDPCNSEKEALYYVYRQLRNAEPADDASAREVITNLFFSDKRYDLGDVGRYRINKKLNLNIDPDIKVLTNEDIIEIIKYLIELVNSKASVDDIDHLSNRRVRTVGEQLYNQFGIGLARMARTVRDRMNVRDNEVFTPIDLVNAKTISSVVNSFFGTNALSQFMDQTNPLAEITHKRRLSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLCVYAKISDLGFITTPYREVKNGKVDFSDNGLKYYTAEEEEEKTVAQGNAPLDENGRFVRERVKARYESDFPLVTPDEVDLMDVSPTQIASIAAALIPFLEHDDANRALMGSNMMRQAVPLLRPESPIVGTGIEGKLVKDSRTQIVAERGGEVVFVDASCIKIRYDRTADEEFVSFDDAIVTYYLPKYRKTNQSTTIDLHPICSKGDRVEAGQILTEGYSTQGGELALGRNVQVAYMPWKGYNYEDAIVLNERMVREDFFTSVHVDEYILEVRETKRGLEELTSDIPNVSEDATRDLDENGIVRIGAHIEPGDILIGKITPKGESDPTPEEKLLRAIFGDKAGDVKDASLKATPSLRGVVIDTKLFSKAAKKKSRTSTKEAVSKLDETYAKRQQQLHERLIEKLTELTKGKTCCGVKDYLNVELIKAGSKFTKKDLEALDFNVIQLSDWTNDAHTNELIKAVAVNYLKHSKEIEAELRRRKLDETIGDELPAGIVQMAKVYIAKKRKIQVGDKMAGRHGNKGIVSKIVRQEDMPFLADGTPVDICLNPLGVPSRMNLGQIFEAVLAWAGRKMNVKFATPIFDGASLNDMNEWTDKAGLPRDGKTYLYDGGTGERFDQPATVGVTYFLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAFGASHILQEILTVKSDDVVGRSKAYEAIVKGDPMPTPGIPESLNVLLHELKGLGLSFSLD

来源 Source

来源生物 organism	Porphyromonas gingivalis
NCBI 分类编号 ncbi_taxonomy_id	837
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	;DNA-directed RNA polymerase subunit beta' ;
分子量 formula_weight	161311.8 kDa
EC 编号 ec_number	2.7.7.6
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	D

MAFRKENKIKNNFSKIRITLASPEEILENSFGEVLKPETINYRTYKPERDGLFCERIFGPVKDFECHCGKYKRIRYRGIVCDRCGVEVTEKKVRRERMGHIHLVVPVAHIWYFRSLPNKIGYLLGLPTKKLDAIIYYERYVVIQPGVAEGLSQLDLLSEEEYLDKLDEIERTHKGNQNLEDTNPDKFIAKIGAEAIYDLLCRVDLDSISYELRDRANTDGSQQRKTEALKRLQVVESFRASKGVNRPEWMVMKVIPVIPPDLRPLVPLDGGRFATSDLNDLYRRVIIRNNRLKRLIEIKAPEVILRNEKRMLQEAVDSLFDNSRKSSAVKSDNNRPLKSLSDSLKGKQGRFRQNLLGKRVDYSARSVIVVGPELKMHECGLPKDMAAELYKPFIIRKLIERGIVKTVKSAKKIVDRKEPVIWDILEYVMKGHPVLLNRAPTLHRLGIQAFQPKLIEGKAIQLHPLSCTAFNADFDGDQMAVHLPLSNEAILEAQLLMLASHNILNPANGAPITVPSQDMVLGLYYITKLRPNTKGHGLIFYGPEEATIAYNEGKVDIHAPIKVYVEDYENGELVRRMVETSVGRLMVNEYVPKKVGYVNEVLGKKALRDIIGSVIKICGVATTAKFLDDIKNLGYYMAFKGGLSFNLADVLIPDEKDQLIQEGYTAVEQIMQDYSMGFITFNERYNQIIDTWTHINGRLSNVLIKQLSSDNDGFNSVFMMMDSGARGSKEQIRQLSGMRGLMAKPQKSGAEGGQIIENPILSNFKEGLSVLEYFISTHGARKGLADTALKTADAGYLTRRLVDVSHDVIITEEDCGTLRGLLTTELKQNEDVVASLYERILGRVSVHDIIHPTTGDIIVRAGEEIREQAAQIIEDSPIEAVEIRSVLTCESKKGVCAKCYGRNLATNRMVQRGEVVGVIAAQSIGEPGTQLTLRTFHVGGIASNVATENSLLSKYDGILEFEELRAVDATDESHQVVVSRMTELRIADPNTGIILANHNIPYGAKLFFRQGDAVKKGDKIIEWDPFNAVIVSEVAGTLSFEGVVENVTFKMESDETTGLKEKIIIESKDKTMAPYARIIDENGEMLKNYSLPMGAHVVKDDGDTVKVGEILVKIPRSVGKAGDITGGLPRVTELFEARNPSNPAIVSEIDGEIGFGKLKRGNREITVTSKLGEEKKYLIPLSKQLLVQENDFVRAGTPLSDGAITPADILAIKGPTAVQEYIVNEVQDVYRLQGVKINDKHFEVIVRQMMRKVEIVDPGDTLFLEQQVVDKFEVMEENDRIWGKKVVIDAGDSQVLKAGQIVTARKLRDENSMLKRKDLKIVKVRDAKSATASQILQGITRAALQTKSFMSAASFQETTKVLNEAAICGKTDYLEGLKENVICGHLIPAGTGLRDYEKLVVMHRDDYEKATAERKSFLSEPTAEPAMEEAPSEHHHHHH

来源 Source

来源生物 organism	Porphyromonas gingivalis
NCBI 分类编号 ncbi_taxonomy_id	837
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	RNA polymerase Rpb6
分子量 formula_weight	12932.5 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	E

MELKKMNVPMDTITRDMVRLSEDTENVYETVMIIAKRANQIGQQMKQDLEKKLQDFSSSNDNLEEVFENREQIEISRYYEHLPKPGLIATAEYEQDKLYHRMPGATSTND

来源 Source

来源生物 organism	Porphyromonas gingivalis
NCBI 分类编号 ncbi_taxonomy_id	837
宿主生物 host_organism	Escherichia coli

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	8dkcA01
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	8dkcB01
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	8dkcD01
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

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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	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	137270

fit	/app/data/saxs_computation/dk/8dkc/8dkc.fit
pddf	/app/data/pr_computation/dk/8dkc/8dkc.pr.out
profile	/app/data/saxs_computation/dk/8dkc/8dkc.dat

P. gingivalis RNA Polymerase

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)