SAXSdb — 7fjk

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

Tyrosine phenol-lyase

Enterobacter agglomerans

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–456 Chain B； UniProt 1–456 Chain C； UniProt 1–456 Chain D； UniProt 1–456	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 4 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 59 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；21 % PEG4000, 0.2 M Ammonium Acetate, 0.1 M Sodium Dihydrogen Citrate, 0.12 M Sodium Hydroxide	Resolution 1.30 Å R-free 0.155

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7FJK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C7G TYROSINE PHENOL-LYASE FROM ERWINIA HERBICOLA Deposited 2000-02-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–456（456 aa） Chain B 1–456（456 aa） Chain C 1–456（456 aa） Chain D 1–456（456 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；30% PEG6000, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 6.2	Resolution 2.10 Å R-free 0.242

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TPL_ENTAG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–456； UniProt 1–456 Author chain B； PDBConstruct 1–456； UniProt 1–456 Author chain C； PDBConstruct 1–456； UniProt 1–456 Author chain D； PDBConstruct 1–456； UniProt 1–456

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	7fjk
Deposition date deposition_date	2021-08-04
Structure title title	Tyrosine phenol-lyase from pantoea agglomerans
Keywords keywords	;Tyrosine, Pyridoxal 5'-phosphate, Phenol, LYASE ;; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.75 Å
Radius of gyration Rg (electron density) rg_electron	36.07 Å
Forward intensity I(0) i0	669474000.00
Molecular weight molecular_weight	210310.0 kDa
Excluded volume excluded_volume	262540 Å³
Envelope volume envelope_volume	307610 Å³
Hydration-shell volume shell_volume	66299 Å³
Envelope diameter envelope_diameter	119.2 Å
Shell Rg shell_rg	45.62 Å
Envelope Rg envelope_rg	36.40 Å
Shape Rg shape_rg	36.10 Å
Total Rg total_rg	36.48 Å
Total atoms total_atoms	14736
Residues n_residues	1824
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	114.8 Å
Rg (real space) rg_real	36.56 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	6.6950e+08
I(0) uncertainty (real space) i0_real_error	1.1870e+07
Rg (reciprocal space) rg_reciprocal	36.68 Å
I(0) (reciprocal space) i0_reciprocal	669600000.0000
Solution quality estimate total_estimate	0.9011
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.4 Å
Skewness Skewness skewness	0.167
Kurtosis Kurtosis kurtosis	-0.525
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	220000000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.937

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Tyrosine phenol-lyase
Molecular weight formula_weight	51429.6 kDa
EC 编号 ec_number	4.1.99.2
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	17301

MNYPAEPFRIKSVETVSMISRDERVKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMIGDEAYAGSENFYHLEKTVKELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRFHQEKNGATFVDIVRDEAHDASLNLPFKGDIDLNKLATLIKEKGAENIAYICLAVTVNLAGGQPVSMANMRAVHEMASTYGIKIFYDATRCVENAYFIKEQEAGYENVSIKDIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDEEMFSAAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLREAGVPIVEPTGGHAVFLDARRFCPHLTQDQFPAQSLAASIYMETGVRSMERGIVSAGRSKETGENHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLTFVYEPKQLRFFTARFDFI

来源 Source

来源生物 organism	Enterobacter agglomerans
NCBI Class编号 ncbi_taxonomy_id	549
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	59

Entity 5 Entity 5 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2042

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7fjkA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	7fjkB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	7fjkC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	7fjkD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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8. Citations (1)

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Unit-cell length a length_a	111.516 Å
Unit-cell length b length_b	161.077 Å
Unit-cell length c length_c	100.146 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	45.840 Å
R factor r_factor	0.1292
R_work r_work	0.1278
R_free r_free	0.1547

fit	/app/data/saxs_computation/fj/7fjk/7fjk.fit
pddf	/app/data/pr_computation/fj/7fjk/7fjk.pr.out
profile	/app/data/saxs_computation/fj/7fjk/7fjk.dat

Tyrosine phenol-lyase from pantoea agglomerans

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

Tyrosine phenol-lyase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction