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3piu

High-resolution structure of native Malus domestica ACC synthase

Method: X-RAY DIFFRACTION Dmax: 73.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

1-aminocyclopropane-1-carboxylate synthase

Malus domestica

UniProt P37821

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–435 Fragment：MdACS-1, UNP residues 1-435 Non-standard monomer：Yes (specific site not provided by mmCIF) PLR (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：293 K；27% MPD (v/v) and 50 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.35 Å R-free 0.171

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 3PIU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B8G 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE Deposited 1999-01-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–431（429 aa）
Chain B 3–431（429 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.37 Å R-free 0.242
1M4N CRYSTAL STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH [2-(AMINO-OXY)ETHYL](5'-DEOXYADENOSIN-5'-YL)(METHYL)SULFONIUM Deposited 2002-07-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–435（435 aa） Fragment：RESIDUES 1-435
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 AAD (2-AMINOOXY-ETHYL)-[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]-METHYL-SULFONIUM × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；MPD, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.01 Å R-free 0.232
1M7Y Crystal structure of apple ACC synthase in complex with L-aminoethoxyvinylglycine Deposited 2002-07-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–435（435 aa） Fragment：RESIDUES 1-435
Not recorded PPG (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；MPD, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.60 Å R-free 0.219
1YNU Crystal structure of apple ACC synthase in complex with L-vinylglycine Deposited 2005-01-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–473（473 aa）
Not recorded NI NICKEL (II) ION × 4 K POTASSIUM ION × 2 PY4 2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 4000, Tris, NiCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.25 Å R-free 0.289
1YNU Crystal structure of apple ACC synthase in complex with L-vinylglycine Deposited 2005-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–473（473 aa）
Not recorded NI NICKEL (II) ION × 2 K POTASSIUM ION × 1 PY4 2-[O-PHOSPHONOPYRIDOXYL]-AMINO- BUTYRIC ACID × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 4000, Tris, NiCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.25 Å R-free 0.289

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

View Construct and Data Evidence
UniProt name 1A1C_MALDO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–435； UniProt 1–435

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3piu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3piu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3piu
Deposition date deposition_date2010-11-08
Structure title titleHigh-resolution structure of native Malus domestica ACC synthase
Keywords keywords;FRUIT RIPENING, ETHYLENE BIOSYNTHESIS, lyase, Pyridoxal 5'-phosphate binding ;; LYASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.73 Å
Radius of gyration Rg (electron density) rg_electron21.68 Å
Forward intensity I(0) i034945700.00
Molecular weight molecular_weight46276.0 kDa
Excluded volume excluded_volume58131 ų
Envelope volume envelope_volume67058 ų
Hydration-shell volume shell_volume25375 ų
Envelope diameter envelope_diameter76.3 Å
Shell Rg shell_rg28.93 Å
Envelope Rg envelope_rg21.95 Å
Shape Rg shape_rg21.69 Å
Total Rg total_rg22.51 Å
Total atoms total_atoms3258
Residues n_residues408
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax73.3 Å
Rg (real space) rg_real22.63 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real3.4950e+07
I(0) uncertainty (real space) i0_real_error4.9020e+05
Rg (reciprocal space) rg_reciprocal22.66 Å
I(0) (reciprocal space) i0_reciprocal34950000.0000
Solution quality estimate total_estimate0.8958
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7 Å
Skewness Skewness skewness0.220
Kurtosis Kurtosis kurtosis-0.438
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8495000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3piua_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (2 domains)

Domain ID domain_id3piuA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id3piuA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
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8. Citations (1)

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9. Files and Curves (10)