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9yit

Crystal structure of glutamate dehydrogenase from Babesia microti in complex with NADP

Method: X-RAY DIFFRACTION Dmax: 134.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate dehydrogenase

Babesia microti strain RI

UniProt A0A0K3AUK4

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 2–467 Chain B； UniProt 2–467 Chain C； UniProt 2–467 Chain D； UniProt 2–467 Chain E； UniProt 2–467 Chain F； UniProt 2–467 Fragment：2-467 PG4 TETRAETHYLENE GLYCOL × 6 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% 3350, 0.1M Bis-Tris 6.5, 0.2M MgCl2. BamiA.17991.a.A21.PW39288 at 16.7 mg/mL. 2mM NADP added to the protein prior to crystallization. plate 19938 F4 drop1, Puck: PSL-0509, Cryo: 12.5% P200 + 87.5% crystallant. Resolution 2.28 Å R-free 0.224

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 9YIT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9YIS Crystal structure of glutamate dehydrogenase from Babesia microti Deposited 2025-10-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 2–467（466 aa） Fragment：2-467
Chain B 2–467（466 aa） Fragment：2-467
Chain C 2–467（466 aa） Fragment：2-467
Chain D 2–467（466 aa） Fragment：2-467
Chain E 2–467（466 aa） Fragment：2-467
Chain F 2–467（466 aa） Fragment：2-467
Not recorded PGE TRIETHYLENE GLYCOL × 6 NA SODIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% 3350, 0.1M BT 6.5, 0.2M sodium acetate. BamiA.17991.a.A21.PW39288 at 16.7 mg/mL. 2mM NADP added to the protein prior to crystallization. plate 19938 D3 drop1, Puck: PSL-0516, Cryo: 12.5% P200 + 87.5% crystallant.
Resolution 2.18 Å R-free 0.209

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

View Construct and Data Evidence
UniProt name A0A0K3AUK4_BABMR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–487； UniProt 2–467 Author chain B； PDBConstruct 22–487； UniProt 2–467 Author chain C； PDBConstruct 22–487； UniProt 2–467 Author chain D； PDBConstruct 22–487； UniProt 2–467 Author chain E； PDBConstruct 22–487； UniProt 2–467 Author chain F； PDBConstruct 22–487； UniProt 2–467

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 9yit

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9yit
Deposition date deposition_date2025-10-02
最后修订 last_revision2025-10-15
Structure title titleCrystal structure of glutamate dehydrogenase from Babesia microti in complex with NADP
Keywords keywords;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, glutamate dehydrogenase, Babesia microti, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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_guinier42.56 Å
Radius of gyration Rg (electron density) rg_electron42.19 Å
Forward intensity I(0) i01406120000.00
Molecular weight molecular_weight307940.0 kDa
Excluded volume excluded_volume384200 ų
Envelope volume envelope_volume481280 ų
Hydration-shell volume shell_volume90265 ų
Envelope diameter envelope_diameter140.6 Å
Shell Rg shell_rg50.27 Å
Envelope Rg envelope_rg42.13 Å
Shape Rg shape_rg42.18 Å
Total Rg total_rg42.54 Å
Total atoms total_atoms21643
Residues n_residues2792
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 dmax134.0 Å
Rg (real space) rg_real42.35 Å
Rg uncertainty (real space) rg_real_error1.07 Å
I(0) (real space) i0_real1.4060e+09
I(0) uncertainty (real space) i0_real_error2.3960e+07
Rg (reciprocal space) rg_reciprocal42.56 Å
I(0) (reciprocal space) i0_reciprocal1406000000.0000
Solution quality estimate total_estimate0.8822
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.3 Å
Skewness Skewness skewness0.183
Kurtosis Kurtosis kurtosis-0.363
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha188000000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.852
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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)