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9z2z

Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae in complex with O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE

Method: X-RAY DIFFRACTION Dmax: 136.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate--tRNA ligase

Chlamydia pneumoniae

UniProt Q9Z7Z3

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 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

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 9Z2Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9Y81 Crystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae Deposited 2025-09-11 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 × 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
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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9z2z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9z2z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9z2z
Deposition date deposition_date2025-11-05
最后修订 last_revision2025-11-26
Structure title titleCrystal structure of Glutamate-tRNA synthetase GluRS from Chlamydia pneumoniae in complex with O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE
Keywords keywords;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Glutamate-tRNA synthetase, Chlamydia pneumoniae, LIGASE ;; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.25 Å
Radius of gyration Rg (electron density) rg_electron39.34 Å
Forward intensity I(0) i0166521000.00
Molecular weight molecular_weight108120.0 kDa
Excluded volume excluded_volume136610 ų
Envelope volume envelope_volume181030 ų
Hydration-shell volume shell_volume41009 ų
Envelope diameter envelope_diameter146.8 Å
Shell Rg shell_rg41.49 Å
Envelope Rg envelope_rg39.89 Å
Shape Rg shape_rg39.38 Å
Total Rg total_rg39.37 Å
Total atoms total_atoms7643
Residues n_residues954
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax136.9 Å
Rg (real space) rg_real39.81 Å
Rg uncertainty (real space) rg_real_error1.44 Å
I(0) (real space) i0_real1.6650e+08
I(0) uncertainty (real space) i0_real_error2.9800e+06
Rg (reciprocal space) rg_reciprocal39.46 Å
I(0) (reciprocal space) i0_reciprocal166500000.0000
Solution quality estimate total_estimate0.7963
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.6 Å
Skewness Skewness skewness0.578
Kurtosis Kurtosis kurtosis-0.279
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18540000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.673; Smooth: 0.579
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)