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1ynu

Crystal structure of apple ACC synthase in complex with L-vinylglycine

Method: X-RAY DIFFRACTION Dmax: 73.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

1-aminocyclopropane-1-carboxylate synthase

Malus x 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 1–473 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–473 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

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 1YNU 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 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 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
3PIU High-resolution structure of native Malus domestica ACC synthase Deposited 2010-11-08 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：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

4 other PDB entries and 4 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 1–473； UniProt 1–473

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 1ynu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ynu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ynu
Deposition date deposition_date2005-01-25
Structure title titleCrystal structure of apple ACC synthase in complex with L-vinylglycine
Keywords keywordsLyase; 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_guinier22.84 Å
Radius of gyration Rg (electron density) rg_electron21.74 Å
Forward intensity I(0) i037213600.00
Molecular weight molecular_weight47478.0 kDa
Excluded volume excluded_volume59549 ų
Envelope volume envelope_volume69292 ų
Hydration-shell volume shell_volume26027 ų
Envelope diameter envelope_diameter74.1 Å
Shell Rg shell_rg29.14 Å
Envelope Rg envelope_rg22.01 Å
Shape Rg shape_rg21.73 Å
Total Rg total_rg22.64 Å
Total atoms total_atoms3333
Residues n_residues417
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 dmax73.0 Å
Rg (real space) rg_real22.73 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real3.7210e+07
I(0) uncertainty (real space) i0_real_error4.1990e+05
Rg (reciprocal space) rg_reciprocal22.76 Å
I(0) (reciprocal space) i0_reciprocal37210000.0000
Solution quality estimate total_estimate0.6923
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.7 Å
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.453
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8658000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 0.130; Positv: 1.000; Valcen: 0.994; Smooth: 0.948
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ynua_
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_id1ynuA01
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_id1ynuA02
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)