6vfd

Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site

Method: X-RAY DIFFRACTION

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

Tryptophan synthase alpha chain

Salmonella typhimurium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Tryptophan synthase beta chain × 2 （A0A5K1VAP1） 1,2-ETHANEDIOL × 8 SERINE × 4 DIMETHYL SULFOXIDE × 20 CHLORIDE ION × 32 (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid × 2 CESIUM ION × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0D6FWC1_SALTM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–268； UniProt 1–268

Tryptophan synthase beta chain

Salmonella typhimurium

UniProt A0A5K1VAP1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Tryptophan synthase alpha chain × 2 （A0A0D6FWC1） 1,2-ETHANEDIOL × 8 SERINE × 4 DIMETHYL SULFOXIDE × 20 CHLORIDE ION × 32 (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid × 2 CESIUM ION × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A5K1VAP1_SALTM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–397； UniProt 1–397

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	6vfd
Deposition date deposition_date	2020-01-03
Structure title title	Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site
Keywords keywords	protein complex, 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.

6vfd__assembly_1__model_1

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

Download this curve (.dat)

6vfd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6vfd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.33 Å
Rg (electron density)	39.77 Å
Total Rg	39.63 Å
Atom count	10041
Residues	1296
Excluded volume	180050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6vfd__assembly_1__model_1`	tetrameric （4）	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 (9)

Entity 1 Entity 1 polymer

Description description	Tryptophan synthase alpha chain
Molecular weight formula_weight	28698.8 kDa
EC 编号 ec_number	4.2.1.20
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	5908

MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMKAASRA

Source Source

Source organism organism	Salmonella typhimurium
Common name common_name	Salmonella enterica subsp. enterica serovar Typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	90371
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tryptophan synthase beta chain
Molecular weight formula_weight	42861.8 kDa
EC 编号 ec_number	4.2.1.20
Mutation mutation	Q114A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTTLLNPYFGEFGGMYVPQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKSEIIAETGAGAHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILDKEGRLPDAVIACVGGGSNAIGMFADFINDTSVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTADGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALEAFKTLCRHEGIIPALESSHALAHALKMMREQPEKEQLLVVNLSGRGDKDIFTVHDILKARGEI

Source Source

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	90371
Host organism host_organism	Escherichia coli

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	4

Entity 4 Entity 4 non-polymer

Description description	SERINE
Molecular weight formula_weight	105.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 7 Entity 7 non-polymer

Description description	(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CESIUM ION
Molecular weight formula_weight	132.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	700

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6vfda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.2 — Ribulose-phoshate binding barrel
Family Family family	c.1.2.4 — Tryptophan biosynthesis enzymes

Domain ID domain_id	d6vfdb_
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

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Unit-cell length a length_a	183.079 Å
Unit-cell length b length_b	59.340 Å
Unit-cell length c length_c	67.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	29.690 Å
R factor r_factor	0.1959
R_work r_work	0.1945
R_free r_free	0.2237

Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site

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

Tryptophan synthase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Tryptophan synthase beta chain

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

6vfd__assembly_1__model_1

6vfd__assembly_1__model_1 | I(q)

6vfd__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site

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

Tryptophan synthase alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tryptophan synthase beta chain

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

6vfd__assembly_1__model_1

6vfd__assembly_1__model_1 | I(q)

6vfd__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)