SAXSdb — 9ymm

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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	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 55–552 Chain D； UniProt 55–552	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

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 9YMM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZPG Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis (Apo) Deposited 2025-12-16	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	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

1 other PDB entries and 1 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 Author chain C； PDBConstruct 22–519； UniProt 55–552 Author chain D； 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	9ymm
Deposition date deposition_date	2025-10-10
最后修订 last_revision	2025-10-22
Structure title title	Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine
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	49.37 Å
Radius of gyration Rg (electron density) rg_electron	48.79 Å
Forward intensity I(0) i0	698740000.00
Molecular weight molecular_weight	218470.0 kDa
Excluded volume excluded_volume	272500 Å³
Envelope volume envelope_volume	407000 Å³
Hydration-shell volume shell_volume	67469 Å³
Envelope diameter envelope_diameter	164.2 Å
Shell Rg shell_rg	56.16 Å
Envelope Rg envelope_rg	47.10 Å
Shape Rg shape_rg	48.78 Å
Total Rg total_rg	49.09 Å
Total atoms total_atoms	15316
Residues n_residues	1897
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	159.3 Å
Rg (real space) rg_real	49.15 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	6.9870e+08
I(0) uncertainty (real space) i0_real_error	1.3890e+07
Rg (reciprocal space) rg_reciprocal	49.37 Å
I(0) (reciprocal space) i0_reciprocal	698900000.0000
Solution quality estimate total_estimate	0.8952
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	69.7 Å
Skewness Skewness skewness	0.046
Kurtosis Kurtosis kurtosis	-0.701
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38610000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.905

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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	58885.5 kDa
EC 编号 ec_number	6.1.1.17
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15316

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	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE
Molecular weight formula_weight	475.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	40

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 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	53.713 Å
Unit-cell length b length_b	124.225 Å
Unit-cell length c length_c	458.212 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.920 Å
Low-resolution limit resolution_low	49.300 Å
R factor r_factor	0.2164
R_work r_work	0.2145
R_free r_free	0.2526

fit	/app/data/saxs_computation/ym/9ymm/9ymm.fit
pddf	/app/data/pr_computation/ym/9ymm/9ymm.pr.out
profile	/app/data/saxs_computation/ym/9ymm/9ymm.dat

Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine

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