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- PDB-1m7y: Crystal structure of apple ACC synthase in complex with L-aminoet... -

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Basic information

Entry
Database: PDB / ID: 1m7y
TitleCrystal structure of apple ACC synthase in complex with L-aminoethoxyvinylglycine
Components1-aminocyclopropane-1-carboxylate synthase
KeywordsLYASE / Fruit ripening / Ethylene biosynthesis / Pyridoxal phosphate
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors / 1-aminocyclopropane-1-carboxylate synthase / 1-aminocyclopropane-1-carboxylate synthase activity / fruit ripening / ethylene biosynthetic process / transaminase activity / pyridoxal phosphate binding / oxidoreductase activity
Similarity search - Function
: / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...: / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PPG / 1-aminocyclopropane-1-carboxylate synthase
Similarity search - Component
Biological speciesMalus x domestica (apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCapitani, G. / McCarthy, D. / Gut, H. / Gruetter, M.G. / Kirsch, J.F.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Apple 1-Aminocyclopropane-1-carboxylate Synthase in Complex with the Inhibitor L-Aminoethoxyvinylglycine
Authors: Capitani, G. / McCarthy, D.L. / Gut, H. / Gruetter, M.G. / Kirsch, J.F.
History
DepositionJul 23, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 28, 2011Group: Non-polymer description
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-aminocyclopropane-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5993
Polymers49,0921
Non-polymers5072
Water5,981332
1
A: 1-aminocyclopropane-1-carboxylate synthase
hetero molecules

A: 1-aminocyclopropane-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1996
Polymers98,1842
Non-polymers1,0154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8130 Å2
ΔGint-36 kcal/mol
Surface area31150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.31, 61.14, 77.14
Angle α, β, γ (deg.)90.00, 123.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

21A-842-

HOH

DetailsThe biological assembly is a dimer

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Components

#1: Protein 1-aminocyclopropane-1-carboxylate synthase / ACC synthase


Mass: 49091.797 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malus x domestica (apple) / Tissue: FRUIT CORTICAL / Plasmid: pET19bV435stopACS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS
References: UniProt: P37821, 1-aminocyclopropane-1-carboxylate synthase
#2: Chemical ChemComp-PPG / (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid


Mass: 389.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N3O8P
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
250 mMHEPES1droppH7.9
310000 mMPLP1drop
41 mMdithiothreitol1drop
54 mMAVG1drop
630 %(v/v)MPD1reservoir
750 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.79955 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79955 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. obs: 50871 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.5
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2684 / % possible all: 76
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 15 Å / Num. obs: 50540
Reflection shell
*PLUS
% possible obs: 76 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B8G

1b8g


Resolution: 1.6→14.924 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used bulk solvent correction (CNS 1.0)
RfactorNum. reflectionSelection details
Rfree0.219 1190 RANDOM
Rwork0.205 --
all-50871 -
obs-50540 -
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.284 Å20 Å23.714 Å2
2---2.589 Å20 Å2
3---2.305 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→14.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 34 332 3724
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection% reflection
Rfree0.317 91 -
Rwork0.277 --
obs-4102 79.4 %
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67

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