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9r4j

CryoEM structure of MraZ in complex with its promoter from Mycoplasma genitalium

Method: ELECTRON MICROSCOPY D_max: 120.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r4j
deposition_date	2025-05-07
title	CryoEM structure of MraZ in complex with its promoter from Mycoplasma genitalium
keywords	MraZ, transcription factor, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	34.95 Å
rg_electron	34.49 Å
i0	143621000.00
molecular_weight	83354.0 kDa
excluded_volume	98834 Å³
envelope_volume	136910 Å³
shell_volume	35198 Å³
envelope_diameter	127.2 Å
shell_rg	38.31 Å
envelope_rg	34.83 Å
shape_rg	34.42 Å
total_rg	34.94 Å
total_atoms	5788
n_residues	607
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	120.5 Å
rg_real	35.22 Å
rg_real_error	1.11 Å
i0_real	1.4360e+08
i0_real_error	2.5680e+06
rg_reciprocal	35.05 Å
i0_reciprocal	143600000.0000
total_estimate	0.8492
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.8 Å
skewness	0.511
kurtosis	-0.349
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	11310000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.842

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Transcriptional regulator MraZ
formula_weight	18496.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D,B,C,A
atom_count	5788

MGSSHHHHHHSSGLVPRGSHMLLGTFNLTLDNKNRISLPAKLRSFFDSSIVINRGFENCLEIRKPADFESYFQTFNNFPNTQKDTRTLKRLIFANANLVELDSANRILIPNNLISDAKLDKEIVLIGQFDHLEVWDKVQYEQYLASSESLETVAERMKDAK

Source

organism	Mycoplasmoides genitalium
ncbi_taxonomy_id	2097
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (33-MER)
formula_weight	10290.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Y

TTTAAAAGTGTCGCAAAGTGTGACAAAGTGGAA

Entity 3 polymer

description	DNA (35-MER)
formula_weight	10607.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Z

TTCCACTTTGTCACACTTTGCGACACTTTTAAACA

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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	3.36 Å
resolution_method	—
num_particles	928675

fit	/app/data/saxs_computation/r4/9r4j/9r4j.fit
pddf	/app/data/pr_computation/r4/9r4j/9r4j.pr.out
profile	/app/data/saxs_computation/r4/9r4j/9r4j.dat

CryoEM structure of MraZ in complex with its promoter from Mycoplasma genitalium

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)