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9v5s

Crystal structure of EF-Tu from Mycoplasma pneumoniae

Method: X-RAY DIFFRACTION D_max: 140.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v5s
deposition_date	2025-05-26
last_revision	2025-10-29
title	Crystal structure of EF-Tu from Mycoplasma pneumoniae
keywords	Mycoplasma pneumoniae, EF-Tu, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	43.98 Å
rg_electron	43.69 Å
i0	434385000.00
molecular_weight	168460.0 kDa
excluded_volume	209990 Å³
envelope_volume	294320 Å³
shell_volume	56613 Å³
envelope_diameter	147.9 Å
shell_rg	48.43 Å
envelope_rg	42.53 Å
shape_rg	43.68 Å
total_rg	43.93 Å
total_atoms	11816
n_residues	1529
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	140.6 Å
rg_real	43.92 Å
rg_real_error	1.13 Å
i0_real	4.3440e+08
i0_real_error	7.8870e+06
rg_reciprocal	43.98 Å
i0_reciprocal	434400000.0000
total_estimate	0.9060
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	50.8 Å
skewness	0.162
kurtosis	-0.726
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	25650000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.909

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Elongation factor Tu
formula_weight	43212.3 kDa
ec_number	3.6.5.3
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	12463

MAREKFDRSKPHVNVGTIGHIDHGKTTLTAAICTVLAKEGKSAATRYDQIDKAPEEKARGITINSAHVEYSSDKRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDSVMPQTREHILLARQVGVPRMVVFLNKCDIATDEEVQELVAEEVRDLLTSYGFDGKNTPIIYGSALKALEGDPKWEAKIHDLMNAVDEWIPTPEREVDKPFLLAIEDTMTITGRGTVVTGRVERGELKVGQEIEIVGLRPIRKAVVTGIEMFKKELDSAMAGDNAGVLLRGVDRKEVERGQVLAKPGSIKPHKKFKAEIYALKKEEGGRHTGFLNGYRPQFYFRTTDVTGSISLPENTEMVLPGDNTSITVELIAPIACEKGSKFSIREGGRTVGAGSVTEVLE

Source

organism	Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)
common_name	Mycoplasmoides pneumoniae
ncbi_taxonomy_id	272634
host_organism	Escherichia coli

Entity 2 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	647

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6. Citations (1)

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length_a	64.382 Å
length_b	106.733 Å
length_c	257.591 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.240 Å
resolution_low	23.200 Å
r_factor	0.2045
r_work	0.2036
r_free	0.2421

fit	/app/data/saxs_computation/v5/9v5s/9v5s.fit
pddf	/app/data/pr_computation/v5/9v5s/9v5s.pr.out
profile	/app/data/saxs_computation/v5/9v5s/9v5s.dat

Crystal structure of EF-Tu from Mycoplasma pneumoniae

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