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- PDB-1b8g: 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1b8g
Title1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE
ComponentsPROTEIN (1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE)
KeywordsLYASE / ETHYLENE BIOSYNTHESIS
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 / 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
PYRIDOXAL-5'-PHOSPHATE / 1-aminocyclopropane-1-carboxylate synthase
Similarity search - Component
Biological speciesMalus x domestica (apple)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.37 Å
AuthorsCapitani, G. / Hohenester, E. / Feng, L. / Storici, P. / Kirsch, J.F. / Jansonius, J.N.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure of 1-aminocyclopropane-1-carboxylate synthase, a key enzyme in the biosynthesis of the plant hormone ethylene.
Authors: Capitani, G. / Hohenester, E. / Feng, L. / Storici, P. / Kirsch, J.F. / Jansonius, J.N.
History
DepositionJan 31, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: PROTEIN (1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE)
B: PROTEIN (1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0224
Polymers96,5282
Non-polymers4942
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-35 kcal/mol
Surface area32040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.630, 69.060, 123.240
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.81007, 0.57723, -0.10289), (0.56896, 0.73147, -0.37581), (-0.14166, -0.36297, -0.92097)
Vector: 17.90037, 32.65306, 180.52733)

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Components

#1: Protein PROTEIN (1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE) / E.C.4.4.1.14 / ACC SYNTHASE / S-ADENOSYL-L-METHIONINE METHYLTHIOADENOSINE-LYASE


Mass: 48263.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malus x domestica (apple) / Tissue: FRUIT CORTICAL TISSUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS
References: UniProt: P37821, 1-aminocyclopropane-1-carboxylate synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 101 TAKEN AS E (SEE CONFLICT FIELD)

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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: 2.4 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
20.2 mMdithiothreitol1drop
30.01 mMPLP1drop
40.01 %(w/v)1dropNaN3
530 mMHEPES1drop
618-24 %(w/v)PEG40001reservoir
750 mMMES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.37→19.7 Å / Num. all: 34176 / Num. obs: 34176 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 32.3 Å2 / Rsym value: 4.7 / Net I/σ(I): 9.8
Reflection shellResolution: 2.37→2.43 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 6.2 / Rsym value: 10.4 / % possible all: 80.8
Reflection
*PLUS
Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 80.8 % / Rmerge(I) obs: 0.104

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.37→19.7 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE BETA ANGLE OF THE UNIT CELL IS VERY CLOSE TO 90 DEGREES. THE SPACEGROUP HAS BEEN CAREFULLY CHECKED AND CONFIRMED AS P21
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1673 4.9 %RANDOM
Rwork0.179 ---
all-34176 --
obs-34176 93.6 %-
Displacement parametersBiso mean: 31.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.37→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6685 0 30 174 6889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.72
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.37→2.48 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.308 228 5.2 %
Rwork0.258 3504 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2HOH.PARHOH.TOP
X-RAY DIFFRACTION3PLP.PARPLP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.72

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