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- PDB-1mhm: Crystal structure of S-adenosylmethionine decarboxylase from potato -

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Basic information

Entry
Database: PDB / ID: 1mhm
TitleCrystal structure of S-adenosylmethionine decarboxylase from potato
Components(S-adenosylmethionine decarboxylase) x 2
KeywordsLYASE / covalent pyruvoyl group
Function / homology
Function and homology information


spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol
Similarity search - Function
S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 ...S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / Dihydrodipicolinate Reductase; domain 2 / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBennett, E.M. / Ekstrom, J.L. / Pegg, A.E. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2002
Title: Monomeric S-Adenosylmethionine Decarboxylase from Plants Provides an Alternative to Putrescine Stimulation
Authors: Bennett, E.M. / Ekstrom, J.L. / Pegg, A.E. / Ealick, S.E.
History
DepositionAug 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: S-adenosylmethionine decarboxylase
A: S-adenosylmethionine decarboxylase


Theoretical massNumber of molelcules
Total (without water)39,7692
Polymers39,7692
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-30 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.650, 71.640, 72.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein S-adenosylmethionine decarboxylase / AdoMetDC / SamDC


Mass: 7886.826 Da / Num. of mol.: 1 / Fragment: beta chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q04694, adenosylmethionine decarboxylase
#2: Protein S-adenosylmethionine decarboxylase / AdoMetDC / SamDC


Mass: 31882.322 Da / Num. of mol.: 1 / Fragment: alpha chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q04694, adenosylmethionine decarboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: trisodium citrate, isopropanol, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Mtrisodium citrate dihydrate1reservoirpH5.6
220 %(v/v)2-propanol1reservoir
320 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. all: 20754 / Num. obs: 18907 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / Rsym value: 0.409 / % possible all: 79.1
Reflection
*PLUS
Num. obs: 17049 / % possible obs: 90.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.26 Å / Lowest resolution: 2.37 Å / % possible obs: 69.6 % / Redundancy: 2.8 % / Num. unique obs: 1084 / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 710 random
Rwork0.218 --
all-14658 -
obs-14658 -
Refine analyzeLuzzati coordinate error free: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 0 84 2444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection
Rfree0.3978 59
Rwork0.289 -
obs-1240
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3pyru.param
X-RAY DIFFRACTION4cis_peptide.param
Refinement
*PLUS
Lowest resolution: 500 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.398 / Num. reflection Rfree: 61 / Num. reflection obs: 1070

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