SAXSdb — 3ceb

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

D-aminoacid aminotransferase-like PLP-dependent enzyme

Haemophilus somnus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q0I0Z6_HAES1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–194； UniProt 1–193

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	3ceb
Deposition date deposition_date	2008-02-28
Structure title title	Crystal structure of a putative 4-amino-4-deoxychorismate lyase (hs_0128) from haemophilus somnus 129pt at 2.40 A resolution
Keywords keywords	;D-aminoacid aminotransferase-like plp-dependent enzymes fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, lyase ;; LYASE
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.

3ceb__assembly_1__model_1

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

Download this curve (.dat)

3ceb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ceb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.36 Å
Rg (electron density)	17.29 Å
Total Rg	18.24 Å
Atom count	1661
Residues	189
Excluded volume	29719 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ceb__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	D-aminoacid aminotransferase-like PLP-dependent enzyme
Molecular weight formula_weight	23669.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1747

GMWQFPLFETILIEQGQAKNISYHQQRYEKSLLKFYPKMKLQPFDLAKIIAKHTALFTHREGLIRCRIDYNHHDYVLQCFPYQQKVYRTFKPVFCDHIDYSLKFSDRTLLNNLLKQKEECDEIMIIRQGKVTDCSIGNLIFRQNNQWITPDKPLLEGTQRAKLLEQKKIIAREIFFEDLAQYEEIRLINAMNGL

Source Source

Source organism organism	Haemophilus somnus
NCBI taxonomy ID ncbi_taxonomy_id	205914
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	5

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	85

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3cebA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain

Domain ID domain_id	3cebA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	10 — D-amino Acid Aminotransferase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-amino Acid Aminotransferase, subunit A, domain 2

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Unit-cell length a length_a	149.730 Å
Unit-cell length b length_b	149.730 Å
Unit-cell length c length_c	34.040 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	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	28.296 Å
R factor r_factor	0.1880
R_work r_work	0.1860
R_free r_free	0.2250

Crystal structure of a putative 4-amino-4-deoxychorismate lyase (hs_0128) from haemophilus somnus 129pt at 2.40 A resolution

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

D-aminoacid aminotransferase-like PLP-dependent enzyme

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

3ceb__assembly_1__model_1

3ceb__assembly_1__model_1 | I(q)

3ceb__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a putative 4-amino-4-deoxychorismate lyase (hs_0128) from haemophilus somnus 129pt at 2.40 A resolution

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

D-aminoacid aminotransferase-like PLP-dependent enzyme

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

3ceb__assembly_1__model_1

3ceb__assembly_1__model_1 | I(q)

3ceb__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)