7mfz

The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Mutant of HCRBPII Bound with LizFluor3 Chromophore Showing Excited State Intermolecular Proton Transfer

Method: X-RAY DIFFRACTION

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

Retinol-binding protein 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	1-(4-{5-[(2E)-but-2-en-2-yl]thiophen-2-yl}phenyl)azetidine × 3 ACETATE ION × 2 GLYCEROL × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RET2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 2–134 Author chain B； PDBConstruct 1–133； UniProt 2–134 Author chain C； PDBConstruct 1–133； UniProt 2–134

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	7mfz
Deposition date deposition_date	2021-04-12
Structure title title	The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Mutant of HCRBPII Bound with LizFluor3 Chromophore Showing Excited State Intermolecular Proton Transfer
Keywords keywords	Domain Swapped Trimer, iLBP, LIPID BINDING PROTEIN; LIPID 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.

7mfz__assembly_1__model_1

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

Download this curve (.dat)

7mfz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7mfz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.20 Å
Rg (electron density)	24.06 Å
Total Rg	24.81 Å
Atom count	3347
Residues	399
Excluded volume	59416 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7mfz__assembly_1__model_1`	trimeric （3）	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	Retinol-binding protein 2
Molecular weight formula_weight	15548.4 kDa
Mutation mutation	Q4F, Q38F, K40D, T53A, R58L, Q108K
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3437

TRDFNGTWEMESNENFEGYMKALDIDFATRKIAVRLTFTDVIDQDGDNFKTKATSTFLNYDVDFTVGVEFDEYTKSLDNRHVKALVTWEGDVLVCVQKGEKENRGWKKWIEGDKLYLELTCGDQVCRQVFKKK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Bacterial expression vector pBEN1-SGC

Entity 2 Entity 2 non-polymer

Description description	1-(4-{5-[(2E)-but-2-en-2-yl]thiophen-2-yl}phenyl)azetidine
Molecular weight formula_weight	269.4 kDa
Source method src_method	syn
Copy count entity_count	3

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	2

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	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	77

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Unit-cell length a length_a	36.932 Å
Unit-cell length b length_b	102.410 Å
Unit-cell length c length_c	108.478 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	12

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.490 Å
Low-resolution limit resolution_low	34.960 Å
R factor r_factor	0.2136
R_work r_work	0.2058
R_free r_free	0.2836

The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Mutant of HCRBPII Bound with LizFluor3 Chromophore Showing Excited State Intermolecular Proton Transfer

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

Retinol-binding protein 2

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

7mfz__assembly_1__model_1

7mfz__assembly_1__model_1 | I(q)

7mfz__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)

The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Mutant of HCRBPII Bound with LizFluor3 Chromophore Showing Excited State Intermolecular Proton Transfer

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

Retinol-binding protein 2

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

7mfz__assembly_1__model_1

7mfz__assembly_1__model_1 | I(q)

7mfz__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)