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9q93

;CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 ;

Method: ELECTRON MICROSCOPY D_max: 233.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q93
deposition_date	2025-02-26
title	;CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 ;
keywords	sigma factor, transcription, complex, AAA+, DNA-binding protein; TRANSCRIPTION
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	66.28 Å
rg_electron	66.75 Å
i0	3224190000.00
molecular_weight	378790.0 kDa
excluded_volume	430510 Å³
envelope_volume	1012600 Å³
shell_volume	131060 Å³
envelope_diameter	235.9 Å
shell_rg	64.41 Å
envelope_rg	63.72 Å
shape_rg	66.77 Å
total_rg	66.64 Å
total_atoms	26918
n_residues	5214
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	233.0 Å
rg_real	66.47 Å
rg_real_error	2.02 Å
i0_real	3.2240e+09
i0_real_error	7.6540e+07
rg_reciprocal	66.08 Å
i0_reciprocal	3222000000.0000
total_estimate	0.8476
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	68.0 Å
skewness	0.417
kurtosis	-0.296
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0002
highest_alpha	400700000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.720

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	Psp operon transcriptional activator
formula_weight	29390.7 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	6,1,2,3,4,5
atom_count	26918

MAEYKDNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSDYPLDDIIIDPFKRRP

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli K-12

Entity 2 polymer

description	RNA polymerase sigma-54 factor
formula_weight	56150.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MGSSHHHHHHSSGLVPRGSHMKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQTDLHDEVEAKEVEDRESLDTVDALEQKEMPDELPLDASWDEIYTAGTPSGNGVDYQDDELPVYQGETTQTLQDYLMWQVELTPFTDTDRAIATSIVDAVDDTGYLTIQIEDIVDSIGDDEIGLEEVEAVLKRIQRFDPVGVAAKDLRDCLLIQLSQFAKETPWLEEARLIISDHLDLLANHDFRTLMRVTRLKEEVLKEAVNLIQSLDPRPGQSIQTSEPEYVIPDVLVRKVSGRWTVELNADSIPRLKINQQYAAMGNSARNDADGQFIRSNLQEARWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASSTAIRALVKKLIAAENPAKPLSDSKLTSMLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV

Source

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli K-12

Entity 3 polymer

description	Non-template DNA (34-MER)
formula_weight	10420.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	N

AGACGGCTGGCACGACTTTTGCAATCGCAGCCCT

Entity 4 polymer

description	Template DNA (34-MER)
formula_weight	10500.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

AGGGCTGATCGTGCAAAAGTCGTGCCAGCCGTCT

Entity 5 polymer

description	DNA-directed RNA polymerase subunit alpha
formula_weight	36558.7 kDa
ec_number	2.7.7.6
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli K-12

Entity 6 polymer

description	DNA-directed RNA polymerase subunit beta
formula_weight	150691.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELED

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli K-12

Entity 7 polymer

description	;DNA-directed RNA polymerase subunit beta' ;
formula_weight	155366.8 kDa
ec_number	2.7.7.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli K-12

Entity 8 polymer

description	DNA-directed RNA polymerase subunit omega
formula_weight	10249.5 kDa
ec_number	2.7.7.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli K-12

Entity 9 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	5

Entity 10 non-polymer

description	ALUMINUM FLUORIDE
formula_weight	84.0 kDa
src_method	syn
entity_count	5

Entity 11 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	5

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	6.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	6.60 Å
resolution_method	—
num_particles	18337

fit	/app/data/saxs_computation/q9/9q93/9q93.fit
pddf	/app/data/pr_computation/q9/9q93/9q93.pr.out
profile	/app/data/saxs_computation/q9/9q93/9q93.dat

;CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)