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- PDB-1iay: CRYSTAL STRUCTURE OF ACC SYNTHASE COMPLEXED WITH COFACTOR PLP AND... -

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Basic information

Entry
Database: PDB / ID: 1iay
TitleCRYSTAL STRUCTURE OF ACC SYNTHASE COMPLEXED WITH COFACTOR PLP AND INHIBITOR AVG
Components1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2
KeywordsLYASE / protein-cofactor-inhibitor complex / V6-dependent enzyme
Function / homology
Function and homology information


1-aminocyclopropane-1-carboxylate synthase / 1-aminocyclopropane-1-carboxylate synthase activity / fruit ripening / ethylene biosynthetic process / amino acid metabolic process / transaminase activity / pyridoxal phosphate binding
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
2-AMINO-4-(2-AMINO-ETHOXY)-BUTYRIC ACID / PYRIDOXAL-5'-PHOSPHATE / 1-aminocyclopropane-1-carboxylate synthase 2
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHuai, Q. / Xia, Y. / Chen, Y. / Callahan, B. / Li, N. / Ke, H.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structures of 1-aminocyclopropane-1-carboxylate (ACC) synthase in complex with aminoethoxyvinylglycine and pyridoxal-5'-phosphate provide new insight into catalytic mechanisms
Authors: Huai, Q. / Xia, Y. / Chen, Y. / Callahan, B. / Li, N. / Ke, H.
History
DepositionMar 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7033
Polymers48,2941
Non-polymers4092
Water82946
1
A: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2
hetero molecules

A: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4076
Polymers96,5882
Non-polymers8194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area7730 Å2
ΔGint-23 kcal/mol
Surface area32460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.1, 123.1, 106.8
Angle α, β, γ (deg.)90, 90, 120
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2 / ACC SYNTHASE 2


Mass: 48294.113 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Plasmid: PET11D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P18485, 1-aminocyclopropane-1-carboxylate synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-AVG / 2-AMINO-4-(2-AMINO-ETHOXY)-BUTYRIC ACID


Mass: 162.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na citrate, 18% PEG3350, 50 mM MgCl2, 10% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Msodium citrate1reservoir
218 %PEG33501reservoir
350 mM1reservoirMgCl2
410 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 13199 / Num. obs: 13199 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 6
Reflection shellResolution: 2.7→2.9 Å / Rmerge(I) obs: 0.445 / % possible all: 76.2
Reflection
*PLUS
Num. measured all: 62671
Reflection shell
*PLUS
% possible obs: 76.2 % / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflectionSelection details
Rfree0.29 1274 random
Rwork0.215 --
all0.215 12258 -
obs0.215 12258 -
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 26 46 3394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0072
X-RAY DIFFRACTIONx_angle_deg1.29
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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