SAXSdb — 1c7g

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

TYROSINE PHENOL-LYASE

Pantoea agglomerans pv. gypsophilae

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	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

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 1C7G	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7FJK Tyrosine phenol-lyase from pantoea agglomerans Deposited 2021-08-04	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 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

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	1c7g
Deposition date deposition_date	2000-02-18
Structure title title	TYROSINE PHENOL-LYASE FROM ERWINIA HERBICOLA
Keywords keywords	;LYASE, TYROSINE DEGRADATION, PYRIDOXAL 5'-PHOSPHATE DEPENDENT ;; 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	37.06 Å
Radius of gyration Rg (electron density) rg_electron	36.39 Å
Forward intensity I(0) i0	645715000.00
Molecular weight molecular_weight	206350.0 kDa
Excluded volume excluded_volume	257390 Å³
Envelope volume envelope_volume	306720 Å³
Hydration-shell volume shell_volume	65847 Å³
Envelope diameter envelope_diameter	117.9 Å
Shell Rg shell_rg	45.70 Å
Envelope Rg envelope_rg	36.57 Å
Shape Rg shape_rg	36.41 Å
Total Rg total_rg	36.81 Å
Total atoms total_atoms	14480
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	115.8 Å
Rg (real space) rg_real	36.86 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	6.4570e+08
I(0) uncertainty (real space) i0_real_error	9.4500e+06
Rg (reciprocal space) rg_reciprocal	36.99 Å
I(0) (reciprocal space) i0_reciprocal	645800000.0000
Solution quality estimate total_estimate	0.9021
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.8 Å
Skewness Skewness skewness	0.163
Kurtosis Kurtosis kurtosis	-0.536
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	215100000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.943

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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	14905

MNYPAEPFRIKSVETVSMISRDERVKKMQEAGYNTFLLNSKDIYIDLLTDSGTNAMSDKQWAGMMIGDEAYAGSENFYHLEKTVKELFGFKHIVPTHQGRGAENLLSQLAIKPGQYVAGNMYFTTTRFHQEKNGATFVDIVRDEAHDASLNLPFKGDIDLNKLATLIKEKGAENIAYICLAVTVNLAGGQPVSMANMRAVHEMASTYGIKIFYDATRCVENAYFIKEQEAGYENVSIKDIVHEMFSYADGCTMSGKKDCLVNIGGFLCMNDEEMFSAAKELVVVYEGMPSYGGLAGRDMEAMAIGLREAMQYEYIEHRVKQVRYLGDKLREAGVPIVEPTGGHAVFLDARRFCPHLTQDQFPAQSLAASIYMETGVRSMERGIVSAGRSKETGENHRPKLETVRLTIPRRVYTYAHMDVVADGIIKLYQHKEDIRGLTFVYEPKQLRFFTARFDFI

来源 Source

来源生物 organism	Pantoea agglomerans pv. gypsophilae
NCBI Class编号 ncbi_taxonomy_id	48984
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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	425

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1c7ga_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.2 — Beta-eliminating lyases

Domain ID domain_id	d1c7gb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.2 — Beta-eliminating lyases

Domain ID domain_id	d1c7gc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.2 — Beta-eliminating lyases

Domain ID domain_id	d1c7gd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.2 — Beta-eliminating lyases

CATH v4.4 (8 domains)

Domain ID domain_id	1c7gA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1c7gA02
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	1c7gB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1c7gB02
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	1c7gC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1c7gC02
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	1c7gD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1c7gD02
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	163.490 Å
Unit-cell length b length_b	113.040 Å
Unit-cell length c length_c	101.090 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	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1862
R_work r_work	0.1862
R_free r_free	0.2420

fit	/app/data/saxs_computation/c7/1c7g/1c7g.fit
pddf	/app/data/pr_computation/c7/1c7g/1c7g.pr.out
profile	/app/data/saxs_computation/c7/1c7g/1c7g.dat

TYROSINE PHENOL-LYASE FROM ERWINIA HERBICOLA

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