SAXSdb — 9zpg

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

Glutamate--tRNA ligase

Moraxella catarrhalis

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 55–552 Chain B； UniProt 55–552	Not recorded	SO4 SULFATE ION × 12 P6G HEXAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；Grid Salt HT B10: 3.0M Ammonium Sulfate 0.1M HEPES pH 7.0, MocaA.01348.a.UX11.PS38771 at 26.6 mg/mL. plate 20153 B10 drop 2, Puck: PSL-1810, Cryo: 2.5 M ammonium sulfate.	Resolution 2.75 Å R-free 0.261

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 9ZPG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YMM Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine Deposited 2025-10-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 55–552（498 aa） Chain B 55–552（498 aa）	Not recorded	GSU O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE × 2 SO4 SULFATE ION × 20 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Grid Salt HT B2: 2.4M ammonium sulfate, 0.1M citrate pH 5.0, MocaA.01348.a.UX11.PS38771 at 26.6 mg/mL. 2mM ligand added prior to crystallization. Plate 20153 B2 drop 1 , Puck: PSL-0805, Cryo: 2.5 M ammonium sulfate.	Resolution 2.92 Å R-free 0.253
9YMM Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine Deposited 2025-10-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 55–552（498 aa） Chain D 55–552（498 aa）	Not recorded	GSU O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE × 2 SO4 SULFATE ION × 20 2PE NONAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Grid Salt HT B2: 2.4M ammonium sulfate, 0.1M citrate pH 5.0, MocaA.01348.a.UX11.PS38771 at 26.6 mg/mL. 2mM ligand added prior to crystallization. Plate 20153 B2 drop 1 , Puck: PSL-0805, Cryo: 2.5 M ammonium sulfate.	Resolution 2.92 Å R-free 0.253

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0AB36DQE3_MORCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–519； UniProt 55–552 Author chain B； PDBConstruct 22–519； UniProt 55–552

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	9zpg
Deposition date deposition_date	2025-12-16
最后修订 last_revision	2025-12-24
Structure title title	Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis (Apo)
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Glutamate--tRNA ligase (GltX), 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	41.55 Å
Radius of gyration Rg (electron density) rg_electron	41.58 Å
Forward intensity I(0) i0	184246000.00
Molecular weight molecular_weight	110170.0 kDa
Excluded volume excluded_volume	137820 Å³
Envelope volume envelope_volume	193130 Å³
Hydration-shell volume shell_volume	42006 Å³
Envelope diameter envelope_diameter	152.6 Å
Shell Rg shell_rg	42.11 Å
Envelope Rg envelope_rg	41.85 Å
Shape Rg shape_rg	41.56 Å
Total Rg total_rg	41.67 Å
Total atoms total_atoms	7739
Residues n_residues	988
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	151.6 Å
Rg (real space) rg_real	42.05 Å
Rg uncertainty (real space) rg_real_error	2.11 Å
I(0) (real space) i0_real	1.8420e+08
I(0) uncertainty (real space) i0_real_error	3.7050e+06
Rg (reciprocal space) rg_reciprocal	41.55 Å
I(0) (reciprocal space) i0_reciprocal	184100000.0000
Solution quality estimate total_estimate	0.7723
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.9 Å
Skewness Skewness skewness	0.626
Kurtosis Kurtosis kurtosis	-0.248
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15860000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.542; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.678; Smooth: 0.731

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Glutamate--tRNA ligase
Molecular weight formula_weight	58885.5 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	7739

MAHHHHHHMGTLEAQTQGPGSMTRPVRTRIAPSPTGFPHVGTAYIALFNLVFAKSMGGEFILRIEDTDQVRSTKQSEQMILDALKWAGLSWAEGPDVGGPHAPYRQSERADIYKKYAEKLLDDGHAFRCFCTPEELDAMREAQMAAGLPVKYDGRYANLSREESDALVAQGKPFVIRMRVPSSGVCTIKDMLRGEVVIPWEQVDMQVLLKTDGLPTYHLANVVDDHLMQITHVLRGEEWLPSAPKHQLLYEYFGWQMPELCHMPLLRNPDKSKLSKRKNPTSITYYRDAGILPEALMNYLGRMGYSLPNEQEKFTLDEMIQSFDIQRISLGGPVFDIEKLYWLNGEYLRTLSVDDLKNKILAWASDDTKLTAIARAIQPRINLLSDAINWAGFYFQNLPAITAEDFAHKSLDNEQILEILYLATWQLENLPIWSEENIYQTLKGLAAHFDIKLKDFMQPFFVAIAGSTSSTPVMNSMYIIGADMTLARLRHACEILGGLGKKKLKKLEEKNKSLPNFLA

来源 Source

来源生物 organism	Moraxella catarrhalis
NCBI Class编号 ncbi_taxonomy_id	480
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	12

Entity 3 Entity 3 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	103.557 Å
Unit-cell length b length_b	53.602 Å
Unit-cell length c length_c	127.962 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.19 °
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	2.750 Å
Low-resolution limit resolution_low	47.070 Å
R factor r_factor	0.2177
R_work r_work	0.2154
R_free r_free	0.2613

fit	/app/data/saxs_computation/zp/9zpg/9zpg.fit
pddf	/app/data/pr_computation/zp/9zpg/9zpg.pr.out
profile	/app/data/saxs_computation/zp/9zpg/9zpg.dat

Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis (Apo)

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