SAXSdb — 3b1f

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

Putative prephenate dehydrogenase

Streptococcus mutans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8DUW0_STRMU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–290； UniProt 1–287

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	3b1f
Deposition date deposition_date	2011-07-02
Structure title title	Crystal structure of prephenate dehydrogenase from Streptococcus mutans
Keywords keywords	enzyme, prephenate, 4-hydroxyphenylpyruvate, oxidative decarboxylation pathway, tyrosine biosynthesis, 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.

3b1f__assembly_1__model_1

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

Download this curve (.dat)

3b1f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b1f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.82 Å
Rg (electron density)	30.04 Å
Total Rg	30.39 Å
Atom count	4564
Residues	558
Excluded volume	81372 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b1f__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 (3)

Entity 1 Entity 1 polymer

Description description	Putative prephenate dehydrogenase
Molecular weight formula_weight	32598.1 kDa
EC 编号 ec_number	1.3.1.12
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	2391

AAAMEEKTIYIAGLGLIGASLALGIKRDHPHYKIVGYNRSDRSRDIALERGIVDEATADFKVFAALADVIILAVPIKKTIDFIKILADLDLKEDVIITDAGSTKYEIVRAAEYYLKDKPVQFVGSHPMAGSHKSGAVAANVNLFENAYYIFSPSCLTKPNTIPALQDLLSGLHARYVEIDAAEHDCVTSQISHFPHIIASSLMKQAGDFSESHEMTKHFAAGGFRDMTRIAESEPGMWTSILLTNQEAVLDRIENFKQRLDEVSNLIKARDENAIWAFFNQSRQIRKNME

Source Source

Source organism organism	Streptococcus mutans
NCBI taxonomy ID ncbi_taxonomy_id	1309
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	109

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3b1fA01
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	3b1fA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3660 — 6-phosphogluconate dehydrogenase C-terminal fold
Homologous superfamily homologous superfamily	10 — 6-phosphogluconate dehydrogenase C-terminal like domain

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Unit-cell length a length_a	79.340 Å
Unit-cell length b length_b	145.624 Å
Unit-cell length c length_c	77.552 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	36.530 Å
R factor r_factor	0.1953
R_work r_work	0.1932
R_free r_free	0.2340

Crystal structure of prephenate dehydrogenase from Streptococcus mutans

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

Putative prephenate dehydrogenase

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

3b1f__assembly_1__model_1

3b1f__assembly_1__model_1 | I(q)

3b1f__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of prephenate dehydrogenase from Streptococcus mutans

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

Putative prephenate dehydrogenase

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

3b1f__assembly_1__model_1

3b1f__assembly_1__model_1 | I(q)

3b1f__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)