SAXSdb — 9yis

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

Glutamate dehydrogenase

Babesia microti strain RI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	TRIETHYLENE GLYCOL × 6 SODIUM ION × 2 TETRAETHYLENE GLYCOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yis
Deposition date deposition_date	2025-10-02
Last revision last_revision	2025-10-15
Structure title title	Crystal structure of glutamate dehydrogenase from Babesia microti
Keywords keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, glutamate dehydrogenase, Babesia microti, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9yis__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9yis__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9yis__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	42.28 Å
Rg (electron density)	41.94 Å
Total Rg	42.32 Å
Atom count	21576
Residues	2800
Excluded volume	384440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9yis__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Glutamate dehydrogenase
Molecular weight formula_weight	53301.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	22270

MAHHHHHHMGTLEAQTQGPGSDYTRSLFTLSGPATASEVEKHIQNAIEFVKRRDPDQVQFIQAFTEVANGLAPVFQTDLKYLEIFLSLSEPERVITFKVPWVNDAGKLMINRGFRVQFNSTLGPYKGGLRFHPSVNLSILKFLGFEQIFKNSLTTLAMGGGKGGSDFDPKGKSDNEVRSFCQSFMTELQRHIGPDTDVPAGDIGVGEREIGFMYGQYKRLSNSSTGTLTGKDPKWGGSFIRPQATGYGLVFFVQYILNDLHNGDSFKGKRVAISGSGNVAQYAADKVIDFGGIPITFSDSSGYIYEPNGFTKEMVTVLMELKNIQRARVSEFLKYSNTAKFFPNKKAWDVDTNVNVALPCACENELDKADAEMLVKKGCIIVGEGANMPTTPEAISVFKAAKVTVCPGKAANAGGVAVSGLEMSQNSQREKWTSEKVLEKLQDIMKNMSKACQEAAAKYNVHGDIISGANIAGFLKVAHSYCDQGCV

Source Source

Source organism organism	Babesia microti strain RI
NCBI taxonomy ID ncbi_taxonomy_id	1133968
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	694

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Unit-cell length a length_a	154.068 Å
Unit-cell length b length_b	197.300 Å
Unit-cell length c length_c	229.680 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	48.580 Å
R factor r_factor	0.1841
R_work r_work	0.1827
R_free r_free	0.2094

Crystal structure of glutamate dehydrogenase from Babesia microti

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

Glutamate dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9yis__assembly_1__model_1

9yis__assembly_1__model_1 | I(q)

9yis__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of glutamate dehydrogenase from Babesia microti

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

Glutamate dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9yis__assembly_1__model_1

9yis__assembly_1__model_1 | I(q)

9yis__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)