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9zum

Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA

Method: X-RAY DIFFRACTION D_max: 94.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zum
deposition_date	2025-12-24
last_revision	2026-02-25
title	Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA
keywords	alphaCTD, RNA polymerase, AT rich DNA, DNA binding, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
method	X-RAY DIFFRACTION

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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	27.31 Å
rg_electron	27.69 Å
i0	46439200.00
molecular_weight	49324.0 kDa
excluded_volume	60251 Å³
envelope_volume	82905 Å³
shell_volume	25956 Å³
envelope_diameter	97.0 Å
shell_rg	33.44 Å
envelope_rg	27.90 Å
shape_rg	27.75 Å
total_rg	28.12 Å
total_atoms	3426
n_residues	412
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	94.1 Å
rg_real	27.33 Å
rg_real_error	0.75 Å
i0_real	4.6440e+07
i0_real_error	6.2910e+05
rg_reciprocal	27.33 Å
i0_reciprocal	46440000.0000
total_estimate	0.8785
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.7 Å
skewness	0.343
kurtosis	-0.261
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	9358000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA-directed RNA polymerase subunit alpha
formula_weight	9283.6 kDa
ec_number	2.7.7.6
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	3597

GSHMNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLAGMGLHLGMDVPNWPPENIED

Source

organism	Caulobacter vibrioides
ncbi_taxonomy_id	155892
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(APAPTPTPAPAPTPTPAPAPTPTPTPTPAPAPTPT)-3') ;
formula_weight	5502.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Y

AATTAATTAATTTTAATT

Entity 3 polymer

description	;DNA (5'-D(APAPTPTPAPAPAPAPTPTPAPAPTPTPAPAPTPT)-3') ;
formula_weight	5520.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

AATTAAAATTAATTAATT

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	171

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6. Citations (1)

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length_a	153.277 Å
length_b	153.277 Å
length_c	32.078 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	20

space_group	P 41
int_tables_number	76
crystal_system	—

resolution	2.430 Å
resolution_low	42.510 Å
r_factor	0.2130
r_work	0.2107
r_free	0.2416

fit	/app/data/saxs_computation/zu/9zum/9zum.fit
pddf	/app/data/pr_computation/zu/9zum/9zum.pr.out
profile	/app/data/saxs_computation/zu/9zum/9zum.dat

Structure of the Caulobacter crescentus RNAP alpha-CTD bound to AT rich DNA

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

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)