SAXSdb — 3d6k

▼

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

Putative aminotransferase

Corynebacterium diphtheriae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 CHLORIDE ION × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 CHLORIDE ION × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6NJY4_CORDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–422； UniProt 1–419 Author chain B； PDBConstruct 4–422； UniProt 1–419 Author chain C； PDBConstruct 4–422； UniProt 1–419 Author chain D； PDBConstruct 4–422； UniProt 1–419

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3d6k
Deposition date deposition_date	2008-05-19
Structure title title	The crystal structure of a putative aminotransferase from Corynebacterium diphtheriae
Keywords keywords	;APC82464, putative aminotransferase, Corynebacterium diphtheriae, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3d6k__assembly_1__model_1

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

Download this curve (.dat)

3d6k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d6k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.18 Å
Rg (electron density)	29.80 Å
Total Rg	30.50 Å
Atom count	6364
Residues	805
Excluded volume	113050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d6k__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d6k__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Putative aminotransferase
Molecular weight formula_weight	46618.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13332

SNAMSLKDYDAARLAQVREEVTAKYAELKAKNLSLDLTRGKPSAEQLDLSNDLLSLPGGDFRTKDGVDCRNYGGLLGIADIRELWAEALGLPADLVVAQDGSSLNIMFDLISWSYTWGNNDSSRPWSAEEKVKWLCPVPGYDRHFTITEHFGFEMINVPMTDEGPDMGVVRELVKDPQVKGMWTVPVFGNPTGVTFSEQTCRELAEMSTAAPDFRIVWDNAYALHTLSDEFPIVHNVIEFAQAAGNPNRFWFMSSTSKITHAGSGVSFFASSKENIEWYASHANVRGIGPNKLNQLAHAQFFGDVAGLKAHMLKHAASLAPKFERVLEILDSRLSEYGVAKWTSPTGGYFISVDVVPGTASRVVELAKEAGIALTGAGSSFPLHNDPNNENIRLAPSLPPVAELEVAMDGFATCVLMAALEV

Source Source

Source organism organism	Corynebacterium diphtheriae
NCBI taxonomy ID ncbi_taxonomy_id	1717
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	683

▼

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3d6kA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	3d6kA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	3d6kB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	3d6kB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	3d6kC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	3d6kC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	3d6kD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	3d6kD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

▶

Unit-cell length a length_a	89.248 Å
Unit-cell length b length_b	56.081 Å
Unit-cell length c length_c	173.592 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	42.680 Å
R factor r_factor	0.1925
R_work r_work	0.1899
R_free r_free	0.2409

The crystal structure of a putative aminotransferase from Corynebacterium diphtheriae

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

Putative aminotransferase

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

3d6k__assembly_1__model_1

3d6k__assembly_1__model_1 | I(q)

3d6k__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

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

The crystal structure of a putative aminotransferase from Corynebacterium diphtheriae

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

Putative aminotransferase

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

3d6k__assembly_1__model_1

3d6k__assembly_1__model_1 | I(q)

3d6k__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

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)