SAXSdb — 3kbc

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

425aa long hypothetical proton glutamate symport protein

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	ASPARTIC ACID × 3 MERCURY (II) ION × 3 SODIUM ION × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O59010_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–425； UniProt 1–425 Author chain B； PDBConstruct 1–425； UniProt 1–425 Author chain C； PDBConstruct 1–425； UniProt 1–425

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	3kbc
Deposition date deposition_date	2009-10-20
Structure title title	Crystal structure of GltPh K55C-A364C mutant crosslinked with divalent mercury
Keywords keywords	AMINO ACID TRANSPORTER, TRANSMEMBRANE TRANSPORTER, ASPARTATE TRANSPORTER, TRANSPORT PROTEIN, CYSTEINE CROSS-LINK, INWARD-FACING; TRANSPORT 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.

3kbc__assembly_1__model_1

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

Download this curve (.dat)

3kbc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kbc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.49 Å
Rg (electron density)	33.01 Å
Total Rg	33.44 Å
Atom count	9096
Residues	1233
Excluded volume	167700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kbc__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 (4)

Entity 1 Entity 1 polymer

Description description	425aa long hypothetical proton glutamate symport protein
Molecular weight formula_weight	44889.2 kDa
Mutation mutation	D37H, K40H, K55C, K125H, K132H, K223H, K264H, C321A, A364C, E368H
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	9096

MGLYRKYIEYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLCMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLCMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTEGELEKGVIA

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ASPARTIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3kbcA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3860 — Proton glutamate symport protein
Homologous superfamily homologous superfamily	10 — Sodium:dicarboxylate symporter

Domain ID domain_id	3kbcB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3860 — Proton glutamate symport protein
Homologous superfamily homologous superfamily	10 — Sodium:dicarboxylate symporter

Domain ID domain_id	3kbcC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3860 — Proton glutamate symport protein
Homologous superfamily homologous superfamily	10 — Sodium:dicarboxylate symporter

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Unit-cell length a length_a	113.142 Å
Unit-cell length b length_b	206.780 Å
Unit-cell length c length_c	205.971 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	24

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

Resolution resolution	3.510 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2670
R_work r_work	0.2670
R_free r_free	0.2700

Crystal structure of GltPh K55C-A364C mutant crosslinked with divalent mercury

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

425aa long hypothetical proton glutamate symport 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

3kbc__assembly_1__model_1

3kbc__assembly_1__model_1 | I(q)

3kbc__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 (4)

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

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of GltPh K55C-A364C mutant crosslinked with divalent mercury

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

425aa long hypothetical proton glutamate symport 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

3kbc__assembly_1__model_1

3kbc__assembly_1__model_1 | I(q)

3kbc__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 (4)

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

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)