SAXSdb — 9rjs

▼

1. Structure Basics

entry_id	9rjs
deposition_date	2025-06-12
title	Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to an analogue of its promoter
keywords	PhiKZ, nvRNAP, RNA, DNA, transcription, RNA BINDING PROTEIN; RNA BINDING PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	45.36 Å
rg_electron	44.54 Å
i0	1389440000.00
molecular_weight	300910.0 kDa
excluded_volume	373070 Å³
envelope_volume	526430 Å³
shell_volume	94314 Å³
envelope_diameter	153.0 Å
shell_rg	52.64 Å
envelope_rg	43.70 Å
shape_rg	44.54 Å
total_rg	44.87 Å
total_atoms	21114
n_residues	2551
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

▼

3. P(r) Analysis (GNOM)

dmax	141.3 Å
rg_real	45.07 Å
rg_real_error	0.69 Å
i0_real	1.3890e+09
i0_real_error	2.2450e+07
rg_reciprocal	45.36 Å
i0_reciprocal	1390000000.0000
total_estimate	0.8908
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	60.6 Å
skewness	0.109
kurtosis	-0.460
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0001
highest_alpha	161500000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.887

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (8)

Entity 1 polymer

description	DNA-directed RNA polymerase,PHIKZ056.1
formula_weight	57976.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	21114

MGSSHHHHHHSSGLVPRGSHMGLYAKVVDHNEVHDQFTGKRIYANDYNTSNSDEKEEFDRHFYSHFQDSEAIESSVSCDCRAIEDAHKLGVICDICNTPVVNTSSRPIEPSMWVRTPKHVRSLINPRLIIMLTGYLVTKEFDFLAYLTDTSYRYDVESIGSKETRRKVDRLLHRGFERGLNHFIDNFNEIFQFLLDANIISNNKSEFAQFVAQNKDKLFPKYLPVPSKLCFVAESTTSGTYLDKPIEAAIDATLTFASIDASSVPLSPIKAQNRTMRGLRLYGQFYEIYAKSRIAQKPGLARRHMFGARLNATARAVITSISDPHDYDELHIPWGVGCQLLKYHLTNKLKAKFNMTTREAFSFVYENVLQYNQIIADLFKELIAEAAPYKGMGCTFHRNPTLQRGSTQQFFITKVKDDINDNSISMSVLCLKAPNADFDGDQLNLTLMPDVYLTKATERIAPHTWVLSIDEPHEISGNLELQGPVVETIINWAHEKYLPPLEEWLKAK

Source

organism	Phikzvirus phiKZ
ncbi_taxonomy_id	169683
host_organism	Escherichia coli

Entity 2 polymer

description	PHIKZ068
formula_weight	59442.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MEIIVTGVQGTGFTEVATEHNGKRLTWTTTAYSKIRVQDQQRVFQEINDYWSGLSAEAQQHIWNCYVEIRKIMDMAMHPMRIAMSLSYYIKEMYKAMPMNSFRRWLLTIGKLYIPVDIEEVITDDSRYNRPDQTYLKHDYINLASVSLALRPLVPIWGEFIDQGTSQEMHKECEVISLISDCEVNHWPVDEISIDGTPVETAYDKLSAYVKFCVEDEAPTLANLYRGMSSAEVPDILQAKVMVRRLTILPLNDATSHSIVSNMFRYVKSNLNPAERSTADRVNDKRPDKGGIDDDDKTSFIESHKTKQRVTPGDIVAYNLDALDVVKLVHKIDDTVPVELIQECLDCVAVTATKDIYPHQILLAQWVMHKAFPARAFSHINKNAVNHLLAAAQSLMWHWGFQQVAVFMQVELYYSGEHAMSIQPRNSTRIQIKYKDVMDELYPHQRQQRAINGVPVAPVNIAGIAVQSAHASIRSSNWIYHGPDRLFKEAEQVTQNKVLVVPATIKSVITELVIHLGKLNQ

Source

organism	Phikzvirus phiKZ
ncbi_taxonomy_id	169683
host_organism	Escherichia coli

Entity 3 polymer

description	PHIKZ071
formula_weight	78780.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSQLGRREIDLTLLGHTGLDPWYGTTSSARGAMFVTHIGQAPEVNGNESRYFLTGAELEYAKYTHDVRFPEDCRVLHVLRKYPTGIGKDSIRSNPVTTIIYENYFDKYKTIGVLHVPEYMSHHQDFGYELVKNREVWETIAPNEMFSKDTVIAQSGAVKKDGTLGMGVNANVVFLSAAGTIEDGFVANKNFLKRMMPTSYSTAVANAGRKAFFLNMYGDDKIYKPFPDIGDVIRPDGVIFAIRDHDDDLAPAEMTPRALRTLDRTFDRAVIGTPGAKVIDIDIWRDERVNPSPTPTGMDAQLVKYHTHLSSYYRELLKIYRGLLARRKDDLHITEEFERLIVTAQMFLPQPDNVRKLSRFYRLDPLDEWRVEVTYKAQKMPAGAFKMTDFHGGKGVICKVMEDEDMPIDENGNRADLIIFGGSTMRRSNYGRIYEHGFGAAARDLAQRLRVEAGLDRHAKPTQQQLNSVMGNTQWVDYAFKELLGFYEIIAPTMHSKMMEHPNPAEHVKTVLMDGFPYIYAPVDDPVDLMAAVNKLINSDKYRPHYGKVSYRDQAGKWVTTKDNVLMGPLYMMLLEKIGEDWSAAASVKTQPFGLPSKLNNADRASTPGRETAIRSFGESETRSYNCTVGPGPTAEILDQTNNPLAHAAVIESWLTAEKPSSVPVAVDREKIPFGGSRPVAMFDHLLECSGIALEYAPDH

Source

organism	Phikzvirus phiKZ
ncbi_taxonomy_id	169683
host_organism	Escherichia coli

Entity 4 polymer

description	PHIKZ074
formula_weight	77513.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MNLNRYKARDLLNLSYDDLWSLPSEWHLIEFDDGKTVVSVDRITKLSVLCWYPLKHYKDCPIPSDHHIDFNRILTDNPKDYLNVEGGRVTSKAMVKHLNKAIWNIYDWSGETVDPEVLSKLAIEGKNWLYNQTTVKLSEYLATLSMFDIAEVYNHPKVREANHNIEPTTYGIEKISYGKVKEVFNDPTQFIGNSIIEGLRSGTQKTEQLLQAFAWRGFPTDINSDIFKYPVTTGYIDGIWNLYENMIESRSGTKALLYNKELLRVTEYFNRKSQLIAQYVQRLHPGDCKTTILAEYPVTKLTLKAFKGKYYQKEDGKLDWIRGNETHLIGTKQKFRSVFGCNHPDSQGICMTCYGRLGINIPKGTNIGQVAAVSMGDKITSAVLSTKHTDASSAVEQYKLGKIESNYLRTGEIPETLYLKKELTQKDYRLVIARSEAENLADILMIDDLTAYPATSATELTSLALVYDDEVNGECGDVLTVSLYNRRASLSIEMLKHIKMVRWELDQRDNIVISLRGFDFNLPFLTLPNKHVNMYEVMKRFQSFLHSGSDSAEAGKLSTEKVGYTSKTYLKNYKSPIEALPVFATMANEKISLNISHCEILIYAMMIRSAQYRDYRLPKPGINGQFEKYNRLMQCRSLGGAMAFEKQHEPLNNPGSFLNKMRNDHPYDLLVKGGKLR

Source

organism	Phikzvirus phiKZ
ncbi_taxonomy_id	169683
host_organism	Escherichia coli

Entity 5 polymer

description	PHIKZ123
formula_weight	62959.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MPDPFLIEKIRENTPCMNPTLANGITVEHTMTRDPNTGVNMTRRYIDSLFDISSVLFPDGFKYEGNRACTPLKHFEEITREYNAKRIANIAPTDMYMIDLMFSYKGEMLYPRPMLLPAFKRGNMVTINGAKYIGSPVLTDVGFSVLNDSIFIPFRRTKLTFKQTDHHYMCNGQRKIMYVIWSQIHNEMAKRTKRDLGNRPHIESCLAHYFFCQFGVTQTFKQWANVDVKCGLLSDFPEEEYPREKWNIYSSATLKGKHPTGEMVLVIPRHQESIFATRLIAGFWYVVDAFPMRFTRPEYVDSTNLWRVILGHMVFGDFEHQGKVEENIDSHLHSFCNSLDEMTIEELKTVGVNVSTIWELLYEIMTSLAHHLYATDIDETSMYGKRLTVLHYLMSEFNYAVSMFGYMFQSRRDREWTVQELNEGLKRSFKLQTAIKRLTVDHGELDTMSNPNSSMLIKGTSILVTQDRAKTAKAHNKSLINDSSRIIHASIAEVGQYKNQPKNNPDGRGRLNMYTKVGPTGLVERREEVREIIDNAQLMFRAK

Source

organism	Phikzvirus phiKZ
ncbi_taxonomy_id	169683
host_organism	Escherichia coli

Entity 6 polymer

description	DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG
formula_weight	23219.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	X

ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG

Entity 7 polymer

description	DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT
formula_weight	22881.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Y

CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT

Entity 8 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

▶

6. Citations (1)

▶

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	triclinic

resolution	2.59 Å
resolution_method	—
num_particles	329400

fit	/app/data/saxs_computation/rj/9rjs/9rjs.fit
pddf	/app/data/pr_computation/rj/9rjs/9rjs.pr.out
profile	/app/data/saxs_computation/rj/9rjs/9rjs.dat

Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to an analogue of its promoter

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

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)