9p4d

Crystal Structure of Engineered glutamine binding protein and a Gd-DOTA ligand - Gln bound

Method: X-RAY DIFFRACTION

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

Amino acid ABC transporter substrate-binding protein

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GLUTAMINE × 1 ACETATE ION × 3 GLYCEROL × 1 4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid × 1 GADOLINIUM ION × 1 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GLUTAMINE × 1 ACETATE ION × 1 GLYCEROL × 2 4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid × 1 GADOLINIUM ION × 1 SULFATE ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	GLUTAMINE × 1 ACETATE ION × 4 GLYCEROL × 1 4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid × 1 GADOLINIUM ION × 1 SULFATE ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GLUTAMINE × 1 GLYCEROL × 1 4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid × 1 GADOLINIUM ION × 1 SULFATE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	GLUTAMINE × 1 ACETATE ION × 1 GLYCEROL × 2 4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid × 1 GADOLINIUM ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	GLUTAMINE × 1 ACETATE ION × 1 GLYCEROL × 2 4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid × 1 GADOLINIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3THM2_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–229； UniProt 23–248 Author chain B； PDBConstruct 4–229； UniProt 23–248 Author chain C； PDBConstruct 4–229； UniProt 23–248 Author chain D； PDBConstruct 4–229； UniProt 23–248 Author chain E； PDBConstruct 4–229； UniProt 23–248 Author chain F； PDBConstruct 4–229； UniProt 23–248

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	9p4d
Deposition date deposition_date	2025-06-16
Structure title title	Crystal Structure of Engineered glutamine binding protein and a Gd-DOTA ligand - Gln bound
Keywords keywords	Amino acid ABC transporter, substrate binding protein, Metal Binding Protein; METAL BINDING PROTEIN
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.

9p4d__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9p4d__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9p4d__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	18.98 Å
Rg (electron density)	17.80 Å
Total Rg	18.90 Å
Atom count	1801
Residues	224
Excluded volume	32094 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9p4d__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9p4d__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9p4d__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9p4d__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`9p4d__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`9p4d__assembly_6__model_1`	monomeric （1）	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 (8)

Entity 1 Entity 1 polymer

Description description	Amino acid ABC transporter substrate-binding protein
Molecular weight formula_weight	25254.7 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	11492

SNAADKKLVVATDTAFVPFEFKQGDIYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITICDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLUTAMINE
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

Description description	4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid
Molecular weight formula_weight	546.6 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	GADOLINIUM ION
Molecular weight formula_weight	157.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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Unit-cell length a length_a	221.437 Å
Unit-cell length b length_b	221.437 Å
Unit-cell length c length_c	79.558 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	hexagonal

Resolution resolution	2.570 Å
Low-resolution limit resolution_low	38.500 Å
R factor r_factor	0.2125
R_work r_work	0.2113
R_free r_free	0.2344

Crystal Structure of Engineered glutamine binding protein and a Gd-DOTA ligand - Gln bound

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

Amino acid ABC transporter substrate-binding protein

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

9p4d__assembly_4__model_1

9p4d__assembly_4__model_1 | I(q)

9p4d__assembly_4__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal Structure of Engineered glutamine binding protein and a Gd-DOTA ligand - Gln bound

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

Amino acid ABC transporter substrate-binding protein

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

9p4d__assembly_4__model_1

9p4d__assembly_4__model_1 | I(q)

9p4d__assembly_4__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)