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9yis

Crystal structure of glutamate dehydrogenase from Babesia microti

Method: X-RAY DIFFRACTION D_max: 131.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yis
deposition_date	2025-10-02
last_revision	2025-10-15
title	Crystal structure of glutamate dehydrogenase from Babesia microti
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	42.28 Å
rg_electron	41.94 Å
i0	1361010000.00
molecular_weight	306750.0 kDa
excluded_volume	384440 Å³
envelope_volume	477850 Å³
shell_volume	90053 Å³
envelope_diameter	139.1 Å
shell_rg	50.20 Å
envelope_rg	41.80 Å
shape_rg	41.93 Å
total_rg	42.32 Å
total_atoms	21576
n_residues	2800
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	131.7 Å
rg_real	42.06 Å
rg_real_error	1.10 Å
i0_real	1.3610e+09
i0_real_error	2.3180e+07
rg_reciprocal	42.27 Å
i0_reciprocal	1361000000.0000
total_estimate	0.8820
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.4 Å
skewness	0.178
kurtosis	-0.372
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	193500000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.821

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	22270

MAHHHHHHMGTLEAQTQGPGSDYTRSLFTLSGPATASEVEKHIQNAIEFVKRRDPDQVQFIQAFTEVANGLAPVFQTDLKYLEIFLSLSEPERVITFKVPWVNDAGKLMINRGFRVQFNSTLGPYKGGLRFHPSVNLSILKFLGFEQIFKNSLTTLAMGGGKGGSDFDPKGKSDNEVRSFCQSFMTELQRHIGPDTDVPAGDIGVGEREIGFMYGQYKRLSNSSTGTLTGKDPKWGGSFIRPQATGYGLVFFVQYILNDLHNGDSFKGKRVAISGSGNVAQYAADKVIDFGGIPITFSDSSGYIYEPNGFTKEMVTVLMELKNIQRARVSEFLKYSNTAKFFPNKKAWDVDTNVNVALPCACENELDKADAEMLVKKGCIIVGEGANMPTTPEAISVFKAAKVTVCPGKAANAGGVAVSGLEMSQNSQREKWTSEKVLEKLQDIMKNMSKACQEAAAKYNVHGDIISGANIAGFLKVAHSYCDQGCV

Source

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

Entity 2 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	694

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6. Citations (1)

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length_a	154.068 Å
length_b	197.300 Å
length_c	229.680 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	48

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.180 Å
resolution_low	48.580 Å
r_factor	0.1841
r_work	0.1827
r_free	0.2094

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