SAXSdb — 4uoy

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

PUTRESCINE AMINOTRANSFERASE

ESCHERICHIA COLI

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 1–459 Chain B； UniProt 1–459 Chain C； UniProt 1–459 Chain D； UniProt 1–459	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 4 FMT FORMIC ACID × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.1 M HEPES PH 7.5 15% PEG 3350 0.2 M SODIUM FORMATE 0.1 MM N-DODECYL-N,N-DIMETHYLGLYCINE	Resolution 2.31 Å R-free 0.233

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 4UOY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4UOX Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate and putrescine Deposited 2014-06-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–459（459 aa） Chain B 1–459（459 aa） Chain C 1–459（459 aa） Chain D 1–459（459 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 4 PUT 1,4-DIAMINOBUTANE × 3 FMT FORMIC ACID × 6 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 15% PEG 3350, 0.2 M SODIUM FORMATE, 0.1 MM N-DODECYL-N,N-DIMETHYLGLYCINE	Resolution 2.08 Å R-free 0.245
5H7D Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex Deposited 2016-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain A 7–453（447 aa） Fragment：UNP RESIDUES 7-453,UNP RESIDUES 220-267 Chain B 7–453（447 aa） Fragment：UNP RESIDUES 7-453,UNP RESIDUES 220-267 Chain C 7–453（447 aa） Fragment：UNP RESIDUES 7-453,UNP RESIDUES 220-267 Chain D 7–453（447 aa） Fragment：UNP RESIDUES 7-453,UNP RESIDUES 220-267	Mutation：N222V, G240A Mutation：N222V, G240A Mutation：N222V, G240A Mutation：N222V, G240A	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；296 K；0.1M HEPES pH 7.5, 20.7% PEG 300, 99mM calcium chloride	Resolution 2.57 Å R-free 0.241
5H7D Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex Deposited 2016-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain I 7–453（447 aa） Fragment：UNP RESIDUES 7-453,UNP RESIDUES 220-267 Chain J 7–453（447 aa） Fragment：UNP RESIDUES 7-453,UNP RESIDUES 220-267 Chain M 7–453（447 aa） Fragment：UNP RESIDUES 7-453,UNP RESIDUES 220-267 Chain N 7–453（447 aa） Fragment：UNP RESIDUES 7-453,UNP RESIDUES 220-267	Mutation：N222V, G240A Mutation：N222V, G240A Mutation：N222V, G240A Mutation：N222V, G240A	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；296 K；0.1M HEPES pH 7.5, 20.7% PEG 300, 99mM calcium chloride	Resolution 2.57 Å R-free 0.241
5X3F Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain Deposited 2017-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain A 7–453（447 aa） Fragment：UNP RESIDUES 7-453,220-269	Mutation：N222V, G240A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；91mM MES pH 5.5, 2.33M Na formate	Resolution 3.38 Å R-free 0.227
8CPL YZw2 a scaffold for cryo-EM of small proteins of interest Deposited 2023-03-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 7–457（451 aa） Chain B 7–457（451 aa） Chain C 7–457（451 aa） Chain D 7–457（451 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16.6% w/v PEG3350, 0.2M NaF and 0.1M Bis-Tris Propane pH 5.5	Resolution 1.60 Å R-free 0.210
8R2P YZwIdeal x16 a scaffold for cryo-EM of small proteins of interest crystallizing in space group 19 (P 21 21 21) Deposited 2023-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 7–457（451 aa） Chain B 7–457（451 aa） Chain C 7–457（451 aa） Chain D 7–457（451 aa）	Mutation：G487A Mutation：G487A Mutation：G487A Mutation：G487A	PLP PYRIDOXAL-5'-PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；50% w/v PEG200, 0.2M MgCl2 and 0.1M Sodium Cacodylate buffer pH 6.5	Resolution 2.22 Å R-free 0.230

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAT_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–459； UniProt 1–459 Author chain B； PDBConstruct 1–459； UniProt 1–459 Author chain C； PDBConstruct 1–459； UniProt 1–459 Author chain D； PDBConstruct 1–459； UniProt 1–459

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	4uoy
Deposition date deposition_date	2014-06-11
Structure title title	Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate
Keywords keywords	TRANSFERASE; TRANSFERASE
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	38.89 Å
Radius of gyration Rg (electron density) rg_electron	38.22 Å
Forward intensity I(0) i0	560125000.00
Molecular weight molecular_weight	196740.0 kDa
Excluded volume excluded_volume	247350 Å³
Envelope volume envelope_volume	291580 Å³
Hydration-shell volume shell_volume	61832 Å³
Envelope diameter envelope_diameter	121.2 Å
Shell Rg shell_rg	45.71 Å
Envelope Rg envelope_rg	38.14 Å
Shape Rg shape_rg	38.20 Å
Total Rg total_rg	38.68 Å
Total atoms total_atoms	13807
Residues n_residues	1810
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	120.6 Å
Rg (real space) rg_real	38.82 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	5.6010e+08
I(0) uncertainty (real space) i0_real_error	9.0460e+06
Rg (reciprocal space) rg_reciprocal	38.87 Å
I(0) (reciprocal space) i0_reciprocal	560200000.0000
Solution quality estimate total_estimate	0.9037
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.2 Å
Skewness Skewness skewness	0.233
Kurtosis Kurtosis kurtosis	-0.716
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	194700000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.931

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PUTRESCINE AMINOTRANSFERASE
Molecular weight formula_weight	50785.3 kDa
EC 编号 ec_number	2.6.1.82
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	14158

MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEALEHHHHHH

来源 Source

来源生物 organism	ESCHERICHIA COLI
NCBI Class编号 ncbi_taxonomy_id	562
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	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	351

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7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	4uoyA01
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	4uoyA02
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	4uoyB01
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	4uoyC01
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	4uoyD01
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	120.945 Å
Unit-cell length b length_b	129.319 Å
Unit-cell length c length_c	131.102 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

Resolution resolution	2.305 Å
Low-resolution limit resolution_low	29.746 Å
R factor r_factor	0.1818
R_work r_work	0.1806
R_free r_free	0.2334

fit	/app/data/saxs_computation/uo/4uoy/4uoy.fit
pddf	/app/data/pr_computation/uo/4uoy/4uoy.pr.out
profile	/app/data/saxs_computation/uo/4uoy/4uoy.dat

Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate

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

PUTRESCINE AMINOTRANSFERASE

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