5dw0

TrpB from Pyrococcus furiosus with L-serine bound as the external aldimine

Method: X-RAY DIFFRACTION

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

Tryptophan synthase beta chain 1

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE × 2 SODIUM ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE × 2 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRPB1_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–388； UniProt 1–388 Author chain B； PDBConstruct 1–388； UniProt 1–388 Author chain C； PDBConstruct 1–388； UniProt 1–388 Author chain D； PDBConstruct 1–388； UniProt 1–388

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	5dw0
Deposition date deposition_date	2015-09-22
Structure title title	TrpB from Pyrococcus furiosus with L-serine bound as the external aldimine
Keywords keywords	PLP, External Aldimine, Pr, 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.

5dw0__assembly_1__model_1

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

Download this curve (.dat)

5dw0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dw0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.83 Å
Rg (electron density)	26.01 Å
Total Rg	26.75 Å
Atom count	5885
Residues	773
Excluded volume	105040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dw0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5dw0__assembly_2__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	Tryptophan synthase beta chain 1
Molecular weight formula_weight	43656.9 kDa
EC 编号 ec_number	4.2.1.20
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	11976

MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHKTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVSGNVLEHHHHHH

Source Source

Source organism organism	Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
Molecular weight formula_weight	336.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	216

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5dw0a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

Domain ID domain_id	d5dw0b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

Domain ID domain_id	d5dw0c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

Domain ID domain_id	d5dw0d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.79 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Superfamily Superfamily superfamily	c.79.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes
Family Family family	c.79.1.1 — Tryptophan synthase beta subunit-like PLP-dependent enzymes

CATH v4.4 (8 domains)

Domain ID domain_id	5dw0A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	5dw0A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	5dw0B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	5dw0B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	5dw0C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	5dw0C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	5dw0D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

Domain ID domain_id	5dw0D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1100 —

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Unit-cell length a length_a	84.241 Å
Unit-cell length b length_b	109.131 Å
Unit-cell length c length_c	160.797 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1781
R_work r_work	0.1758
R_free r_free	0.2212

TrpB from Pyrococcus furiosus with L-serine bound as the external aldimine

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

Tryptophan synthase beta chain 1

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

5dw0__assembly_1__model_1

5dw0__assembly_1__model_1 | I(q)

5dw0__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

TrpB from Pyrococcus furiosus with L-serine bound as the external aldimine

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

Tryptophan synthase beta chain 1

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

5dw0__assembly_1__model_1

5dw0__assembly_1__model_1 | I(q)

5dw0__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)