SAXSdb — 8v9p

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

Tryptophanase

Proteus vulgaris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	POTASSIUM ION × 4 ;(2~{E})-2-[(~{Z})-[2-methyl-3-oxidanyl-5-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]-1~{H}-pyridin-4-ylidene]methyl]imino-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-1~{H}-indol-3-yl]propanoic acid ; × 4 DIMETHYL SULFOXIDE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TNAA_PROVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–467； UniProt 1–467 Author chain B； PDBConstruct 1–467； UniProt 1–467 Author chain C； PDBConstruct 1–467； UniProt 1–467 Author chain D； PDBConstruct 1–467； UniProt 1–467

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	8v9p
Deposition date deposition_date	2023-12-08
Structure title title	Proteus vulgaris tryptophan indole-lyase complexed with (3S)-dioxindolyl-L-alanine
Keywords keywords	;pyridoxal-5'-phosphate, fold I, tetramer, 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.

8v9p__assembly_1__model_1

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

Download this curve (.dat)

8v9p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8v9p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.03 Å
Rg (electron density)	36.44 Å
Total Rg	36.89 Å
Atom count	14888
Residues	1864
Excluded volume	265830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8v9p__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 (5)

Entity 1 Entity 1 polymer

Description description	Tryptophanase
Molecular weight formula_weight	52559.0 kDa
EC 编号 ec_number	4.1.99.1
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	16188

MAKRIVEPFRIKMVEKIRVPSREEREAALKEAGYNPFLLPSSAVYIDLLTDSGTNAMSDHQWAAMITGDEAYAGSRNYYDLKDKAKELFNYDYIIPAHQGRGAENILFPVLLKYKQKEGKAKNPVFISNFHFDTTAAHVELNGCKAINIVTEKAFDSETYDDWKGDFDIKKLKENIAQHGADNIVAIVSTVTCNSAGGQPVSMSNLKEVYEIAKQHGIFVVMDSARFCENAYFIKARDPKYKNATIKEVIFDMYKYADALTMSAKKDPLLNIGGLVAIRDNEEIFTLARQRCVPMEGFVTYGGLAGRDMAAMVQGLEEGTEEEYLHYRIGQVKYLGDRLREAGIPIQYPTGGHAVFVDCKKLVPQIPGDQFPAQAVINALYLESGVRAVEIGSFLLGRDPATGEQKHADMEFMRLTIARRVYTNDHMDYIADALIGLKEKFATLKGLEFEYEPPVLRHFTARLKPIE

Source Source

Source organism organism	Proteus vulgaris
NCBI taxonomy ID ncbi_taxonomy_id	585
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	;(2~{E})-2-[(~{Z})-[2-methyl-3-oxidanyl-5-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]-1~{H}-pyridin-4-ylidene]methyl]imino-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-1~{H}-indol-3-yl]propanoic acid ;
Molecular weight formula_weight	465.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1126

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Unit-cell length a length_a	67.342 Å
Unit-cell length b length_b	112.717 Å
Unit-cell length c length_c	119.518 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	61.870 Å
R factor r_factor	0.2014
R_work r_work	0.1990
R_free r_free	0.2466

Proteus vulgaris tryptophan indole-lyase complexed with (3S)-dioxindolyl-L-alanine

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

Tryptophanase

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

8v9p__assembly_1__model_1

8v9p__assembly_1__model_1 | I(q)

8v9p__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Proteus vulgaris tryptophan indole-lyase complexed with (3S)-dioxindolyl-L-alanine

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

Tryptophanase

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

8v9p__assembly_1__model_1

8v9p__assembly_1__model_1 | I(q)

8v9p__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)