SAXSdb — 9y81

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate--tRNA ligase

Chlamydia pneumoniae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–505 Chain B； UniProt 1–505	Not recorded	SO4 SULFATE ION × 6 CL CHLORIDE ION × 13 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；JCSG+ H7: 0.20 M ammonium sulfate, 0.10 M Bis-Tris, pH 5.5, 25% PEG 3350. ChpnA.01348.a.UX11.PS38780 at 9.1 mg/mL. plate 20178 H7 d2, Puck: PSL-1705, Cryo: 20% ethylene glycol + 80% crystallant	Resolution 2.08 Å R-free 0.233

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9Y81	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Z2X Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae (Orthorhombic C form) Deposited 2025-11-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–505（505 aa）	Not recorded	CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；0.1M NaCH3COO/CH3COOH pH 5.0, 2% PEG 4000, 15% MPD. ChpnA.01348.a.UX11.PS38780 at 8 mg/mL. 2 mM ATP added to the protein prior to crystallization. plate 20340 E8 drop 1, Puck: PSL-1216, Cryo: 25% MPD + 75% crystallant	Resolution 2.75 Å R-free 0.265
9Z2Y Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae in complex with ATP Deposited 2025-11-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–505（505 aa） Chain B 1–505（505 aa）	Not recorded	SO4 SULFATE ION × 6 CL CHLORIDE ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；JCSG+ H7: 0.20 M ammonium sulfate, 0.10 M Bis-Tris, pH 5.5, 25% PEG 3350. ChpnA.01348.a.UX11.PS38780 at 8 mg/mL. 2 mM ATP added to the protein prior to crystallization. ATP only bound in one subunit. plate 20308 F10 drop2, Puck: PSL-0302, Cryo: 33% (w/v) PEG 3350, 0.1M Bis-Tris pH 5.5, 0.2M Ammonium Sulfate	Resolution 2.65 Å R-free 0.264
9Z2Z Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae in complex with O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE Deposited 2025-11-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–505（505 aa） Chain B 1–505（505 aa）	Not recorded	GSU O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；Proplex F1: 0.1M HEPES pH 7.0, 20% PEG 8000. ChpnA.01348.a.UX11.PS38780 at 8 mg/mL. 2 mM GSU added to the protein prior to crystallization. 20179 F1 drop 1, Puck: PSL-0609, Cryo: 20% glycerol + 80% crystallant	Resolution 2.80 Å R-free 0.254

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYE_CHLPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–526； UniProt 1–505 Author chain B； PDBConstruct 22–526； UniProt 1–505

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9y81
Deposition date deposition_date	2025-09-11
最后修订 last_revision	2025-09-24
Structure title title	Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.76 Å
Radius of gyration Rg (electron density) rg_electron	39.88 Å
Forward intensity I(0) i0	178246000.00
Molecular weight molecular_weight	111300.0 kDa
Excluded volume excluded_volume	140430 Å³
Envelope volume envelope_volume	190320 Å³
Hydration-shell volume shell_volume	42421 Å³
Envelope diameter envelope_diameter	148.2 Å
Shell Rg shell_rg	41.80 Å
Envelope Rg envelope_rg	40.43 Å
Shape Rg shape_rg	39.85 Å
Total Rg total_rg	40.10 Å
Total atoms total_atoms	7835
Residues n_residues	962
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	139.2 Å
Rg (real space) rg_real	40.33 Å
Rg uncertainty (real space) rg_real_error	1.44 Å
I(0) (real space) i0_real	1.7820e+08
I(0) uncertainty (real space) i0_real_error	3.4490e+06
Rg (reciprocal space) rg_reciprocal	39.99 Å
I(0) (reciprocal space) i0_reciprocal	178200000.0000
Solution quality estimate total_estimate	0.5696
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.3 Å
Skewness Skewness skewness	0.578
Kurtosis Kurtosis kurtosis	-0.271
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20800000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.699; Smooth: 0.561

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Glutamate--tRNA ligase
Molecular weight formula_weight	60568.1 kDa
EC 编号 ec_number	6.1.1.17
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8102

MAHHHHHHMGTLEAQTQGPGSMNWENVRVRVAPSPTGDPHVGTAYMALFNEIFAKRFKGKMILRIEDTDRTRSRQDYEENIFSALRWCGIQWDEGPDVGGPYGPYRQSERTKIYQGYVETLLKTDCAYKCFATPQELAEMRAVASTLGYRGGYDRRYRYLSPEEVASREAAGQPYTIRLKVPLSGECVFEDYSKGRVVFPWADVDDQVLVKSDGFPTYHFANVIDDHLMGITHVLRGEEWLSSTPKHLLLYEAFGWEPPVFLHMPLLLNPDGTKLSKRKNPTSIFYYRDSGYVKEAFVNFLTLMGYSMEGDEEVYSLERIIETFNPRRIGKSGAVFDIQKLDWMNKHYLNHEGSPECLLKELQGWLLNDEFFLKILPLCQSRITTLAEFINLTSFFFSGLLEYRVEELLPQALSPEKAAILLYSYVKYLEKTDQWTKETCYLGSKWLAQAFNVHHKKAIIPLLYVAITGKKQGLPLFDSIEILGKPRARARLVYAEKLLGGVPKKLAATVDKFMQREDFEEATFDL

来源 Source

来源生物 organism	Chlamydia pneumoniae
NCBI Class编号 ncbi_taxonomy_id	83558
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	264

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8. Citations (1)

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Unit-cell length a length_a	50.693 Å
Unit-cell length b length_b	130.099 Å
Unit-cell length c length_c	93.014 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	49.140 Å
R factor r_factor	0.1846
R_work r_work	0.1822
R_free r_free	0.2333

fit	/app/data/saxs_computation/y8/9y81/9y81.fit
pddf	/app/data/pr_computation/y8/9y81/9y81.pr.out
profile	/app/data/saxs_computation/y8/9y81/9y81.dat

Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate--tRNA ligase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction