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- PDB-1m4n: CRYSTAL STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH [2-(AMINO... -

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Basic information

Entry
Database: PDB / ID: 1m4n
TitleCRYSTAL STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH [2-(AMINO-OXY)ETHYL](5'-DEOXYADENOSIN-5'-YL)(METHYL)SULFONIUM
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 / fruit ripening / 1-aminocyclopropane-1-carboxylate synthase activity / 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 / Pyridoxal phosphate-dependent transferase, major 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-AAD / PYRIDOXAL-5'-PHOSPHATE / 1-aminocyclopropane-1-carboxylate synthase
Similarity search - Component
Biological speciesMalus x domestica (apple)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsCapitani, G. / Eliot, A.C. / Gut, H. / Khomutov, R.M. / Kirsch, J.F. / Grutter, M.G.
CitationJournal: BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS / Year: 2003
Title: Structure of 1-aminocyclopropane-1-carboxylate synthase in complex with an amino-oxy analogue of the substrate: implications for substrate binding.
Authors: Capitani, G. / Eliot, A.C. / Gut, H. / Khomutov, R.M. / Kirsch, J.F. / Grutter, M.G.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,8924
Polymers49,0921
Non-polymers8003
Water5,188288
1
A: 1-aminocyclopropane-1-carboxylate synthase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)99,7838
Polymers98,1842
Non-polymers1,6006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8910 Å2
ΔGint-19 kcal/mol
Surface area30600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.00, 61.33, 76.94
Angle α, β, γ (deg.)90.00, 123.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-813-

HOH

21A-817-

HOH

31A-838-

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: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P37821, 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-AAD / (2-AMINOOXY-ETHYL)-[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]-METHYL-SULFONIUM / 5'-[[2-(AMINOOXY)ETHYL]METHYLSULFONIO]-5'-DEOXY-ADENOSINE / [2-(AMINO-OXY)ETHYL](5'-DEOXYADENOSIN-5'-YL)(METHYL)SULFONIUM


Mass: 357.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N6O4S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
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
120 mg/mlprotein1drop
210 mMAMA1drop
350 mMHEPES1droppH7.9
410000 nmPLP1drop
51 mMdithiothreitol1drop
630 %(v/v)MPD1reservoir
750 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 30, 2000 / Details: double focussing mirrors (Prophysics)
RadiationMonochromator: MIRRORS (PROPHYSICS) + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→23.77 Å / Num. obs: 26106 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.6
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / Num. unique all: 1185 / % possible all: 66.5
Reflection
*PLUS
Lowest resolution: 24 Å
Reflection shell
*PLUS
% possible obs: 66.5 % / Rmerge(I) obs: 0.29

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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: 2.01→23.77 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. reflection% reflectionSelection details
Rfree0.232 704 2.7 %RANDOM
Rwork0.199 ---
obs-26106 96.2 %-
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.231 Å20 Å23.166 Å2
2---2.25 Å20 Å2
3---2.481 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.01→23.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 51 288 3677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 2.01→2.08 Å
RfactorNum. reflection% reflection
Rfree0.406 59 -
Rwork0.347 1857 -
obs-1857 68.5 %
Refinement
*PLUS
Lowest resolution: 24 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67
LS refinement shell
*PLUS
Lowest resolution: 2.06 Å

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