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9z2y

Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae in complex with ATP

Method: X-RAY DIFFRACTION D_max: 137.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z2y
deposition_date	2025-11-05
last_revision	2025-11-26
title	Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae in complex with ATP
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Glutamate-tRNA synthetase, Chlamydia pneumoniae, LIGASE ;; LIGASE
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	39.24 Å
rg_electron	39.44 Å
i0	171171000.00
molecular_weight	109250.0 kDa
excluded_volume	137930 Å³
envelope_volume	178900 Å³
shell_volume	40770 Å³
envelope_diameter	146.0 Å
shell_rg	41.19 Å
envelope_rg	39.64 Å
shape_rg	39.45 Å
total_rg	39.52 Å
total_atoms	7709
n_residues	950
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	137.7 Å
rg_real	39.79 Å
rg_real_error	1.56 Å
i0_real	1.7120e+08
i0_real_error	3.2250e+06
rg_reciprocal	39.45 Å
i0_reciprocal	171100000.0000
total_estimate	0.5688
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	34.4 Å
skewness	0.574
kurtosis	-0.290
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	21290000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.687; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.663; Smooth: 0.625

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glutamate--tRNA ligase
formula_weight	60568.1 kDa
ec_number	6.1.1.17
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7709

MAHHHHHHMGTLEAQTQGPGSMNWENVRVRVAPSPTGDPHVGTAYMALFNEIFAKRFKGKMILRIEDTDRTRSRQDYEENIFSALRWCGIQWDEGPDVGGPYGPYRQSERTKIYQGYVETLLKTDCAYKCFATPQELAEMRAVASTLGYRGGYDRRYRYLSPEEVASREAAGQPYTIRLKVPLSGECVFEDYSKGRVVFPWADVDDQVLVKSDGFPTYHFANVIDDHLMGITHVLRGEEWLSSTPKHLLLYEAFGWEPPVFLHMPLLLNPDGTKLSKRKNPTSIFYYRDSGYVKEAFVNFLTLMGYSMEGDEEVYSLERIIETFNPRRIGKSGAVFDIQKLDWMNKHYLNHEGSPECLLKELQGWLLNDEFFLKILPLCQSRITTLAEFINLTSFFFSGLLEYRVEELLPQALSPEKAAILLYSYVKYLEKTDQWTKETCYLGSKWLAQAFNVHHKKAIIPLLYVAITGKKQGLPLFDSIEILGKPRARARLVYAEKLLGGVPKKLAATVDKFMQREDFEEATFDL

Source

organism	Chlamydia pneumoniae
ncbi_taxonomy_id	83558
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	49.946 Å
length_b	132.078 Å
length_c	92.340 Å
angle_alpha	90.00 °
angle_beta	104.23 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.650 Å
resolution_low	48.410 Å
r_factor	0.2137
r_work	0.2112
r_free	0.2638

fit	/app/data/saxs_computation/z2/9z2y/9z2y.fit
pddf	/app/data/pr_computation/z2/9z2y/9z2y.pr.out
profile	/app/data/saxs_computation/z2/9z2y/9z2y.dat

Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae in complex with ATP

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