SAXSdb — 2htd

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

;Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase ;

Lactobacillus delbrueckii subsp. bulgaricus

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 × 6 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q1GBW8_LACDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–140； UniProt 1–121 Author chain B； PDBConstruct 20–140； UniProt 1–121

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	2htd
Deposition date deposition_date	2006-07-25
Structure title title	CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION
Keywords keywords	;PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

2htd__assembly_1__model_1

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

Download this curve (.dat)

2htd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2htd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.08 Å
Rg (electron density)	18.08 Å
Total Rg	18.87 Å
Atom count	1905
Residues	242
Excluded volume	33819 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2htd__assembly_1__model_1`	dimeric （2）	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	;Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase ;
Molecular weight formula_weight	15800.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2156

MGSDKIHHHHHHENLYFQGMKKLNTNKLTEEQVNLFKNNLVYLATVDADGNPQVGPKGSMTVLDPSHLQYLEKTKGEAYENIKRGSKVALVAADVPSHTAVRVLATAEVHEDDDYAKKVLAKTEFPNAFVVNLNIEEVFA

Source Source

Source organism organism	Lactobacillus delbrueckii subsp. bulgaricus
NCBI taxonomy ID ncbi_taxonomy_id	321956
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	6

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	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	205

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2htdA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

Domain ID domain_id	2htdB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

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Unit-cell length a length_a	34.104 Å
Unit-cell length b length_b	71.123 Å
Unit-cell length c length_c	47.031 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	39.253 Å
R factor r_factor	0.1600
R_work r_work	0.1580
R_free r_free	0.2060

CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION

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

;Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase ;

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

2htd__assembly_1__model_1

2htd__assembly_1__model_1 | I(q)

2htd__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 PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION

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

;Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase ;

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

2htd__assembly_1__model_1

2htd__assembly_1__model_1 | I(q)

2htd__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)