SAXSdb — 2qyt

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

2-dehydropantoate 2-reductase

Porphyromonas gingivalis

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 1,2-ETHANEDIOL × 5 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7MT04_PORGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–317； UniProt 1–314

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	2qyt
Deposition date deposition_date	2007-08-15
Structure title title	Crystal structure of 2-dehydropantoate 2-reductase from Porphyromonas gingivalis W83
Keywords keywords	;APC81190, 2-dehydropantoate 2-reductase, Porphyromonas gingivalis W83, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

2qyt__assembly_1__model_1

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

Download this curve (.dat)

2qyt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qyt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.88 Å
Rg (electron density)	19.76 Å
Total Rg	20.51 Å
Atom count	2286
Residues	277
Excluded volume	41134 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qyt__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	2-dehydropantoate 2-reductase
Molecular weight formula_weight	35671.9 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	2467

SNAMNQQPIKIAVFGLGGVGGYYGAMLALRAAATDGLLEVSWIARGAHLEAIRAAGGLRVVTPSRDFLARPTCVTDNPAEVGTVDYILFCTKDYDMERGVAEIRPMIGQNTKILPLLNGADIAERMRTYLPDTVVWKGCVYISARKSAPGLITLEADRELFYFGSGLPEQTDDEVRLAELLTAAGIRAYNPTDIDWYIMKKFMMISVTATATAYFDKPIGSILTEHEPELLSLLEEVAELFRAKYGQVPDDVVQQLLDKQRKMPPESTSSMHSDFLQGGSTEVETLTGYVVREAEALRVDLPMYKRMYRELVSRTAN

Source Source

Source organism organism	Porphyromonas gingivalis
NCBI taxonomy ID ncbi_taxonomy_id	242619
Host organism host_organism	Escherichia coli BL21

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	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2qytA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2qytA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

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Unit-cell length a length_a	79.577 Å
Unit-cell length b length_b	79.577 Å
Unit-cell length c length_c	98.260 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	41.810 Å
R factor r_factor	0.1984
R_work r_work	0.1949
R_free r_free	0.2648

Crystal structure of 2-dehydropantoate 2-reductase from Porphyromonas gingivalis W83

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

2-dehydropantoate 2-reductase

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

2qyt__assembly_1__model_1

2qyt__assembly_1__model_1 | I(q)

2qyt__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 2-dehydropantoate 2-reductase from Porphyromonas gingivalis W83

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

2-dehydropantoate 2-reductase

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

2qyt__assembly_1__model_1

2qyt__assembly_1__model_1 | I(q)

2qyt__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)