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9yit

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

Method: X-RAY DIFFRACTION D_max: 134.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yit
deposition_date	2025-10-02
last_revision	2025-10-15
title	Crystal structure of glutamate dehydrogenase from Babesia microti in complex with NADP
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, glutamate dehydrogenase, Babesia microti, OXIDOREDUCTASE ;; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	42.56 Å
rg_electron	42.19 Å
i0	1406120000.00
molecular_weight	307940.0 kDa
excluded_volume	384200 Å³
envelope_volume	481280 Å³
shell_volume	90265 Å³
envelope_diameter	140.6 Å
shell_rg	50.27 Å
envelope_rg	42.13 Å
shape_rg	42.18 Å
total_rg	42.54 Å
total_atoms	21643
n_residues	2792
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	134.0 Å
rg_real	42.35 Å
rg_real_error	1.07 Å
i0_real	1.4060e+09
i0_real_error	2.3960e+07
rg_reciprocal	42.56 Å
i0_reciprocal	1406000000.0000
total_estimate	0.8822
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.3 Å
skewness	0.183
kurtosis	-0.363
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	188000000.0000
n_real_points	38
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glutamate dehydrogenase
formula_weight	53301.4 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	21896

MAHHHHHHMGTLEAQTQGPGSDYTRSLFTLSGPATASEVEKHIQNAIEFVKRRDPDQVQFIQAFTEVANGLAPVFQTDLKYLEIFLSLSEPERVITFKVPWVNDAGKLMINRGFRVQFNSTLGPYKGGLRFHPSVNLSILKFLGFEQIFKNSLTTLAMGGGKGGSDFDPKGKSDNEVRSFCQSFMTELQRHIGPDTDVPAGDIGVGEREIGFMYGQYKRLSNSSTGTLTGKDPKWGGSFIRPQATGYGLVFFVQYILNDLHNGDSFKGKRVAISGSGNVAQYAADKVIDFGGIPITFSDSSGYIYEPNGFTKEMVTVLMELKNIQRARVSEFLKYSNTAKFFPNKKAWDVDTNVNVALPCACENELDKADAEMLVKKGCIIVGEGANMPTTPEAISVFKAAKVTVCPGKAANAGGVAVSGLEMSQNSQREKWTSEKVLEKLQDIMKNMSKACQEAAAKYNVHGDIISGANIAGFLKVAHSYCDQGCV

Source

organism	Babesia microti strain RI
ncbi_taxonomy_id	1133968
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	743.4 kDa
src_method	syn
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	253

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6. Citations (1)

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length_a	105.667 Å
length_b	125.313 Å
length_c	123.706 Å
angle_alpha	90.00 °
angle_beta	100.29 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.280 Å
resolution_low	48.020 Å
r_factor	0.1919
r_work	0.1902
r_free	0.2235

fit	/app/data/saxs_computation/yi/9yit/9yit.fit
pddf	/app/data/pr_computation/yi/9yit/9yit.pr.out
profile	/app/data/saxs_computation/yi/9yit/9yit.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction