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- PDB-1msv: The S68A S-adenosylmethionine decarboxylase proenzyme processing ... -

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Basic information

Entry
Database: PDB / ID: 1msv
TitleThe S68A S-adenosylmethionine decarboxylase proenzyme processing mutant.
ComponentsS-adenosylmethionine decarboxylase proenzyme
KeywordsLYASE / spermidine biosynthesis / decarboxylase / pyruvate / s-adenosylmethionine / sandwich / allosteric enzyme / pyruvoyl
Function / homology
Function and homology information


spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / putrescine binding / spermidine biosynthetic process / identical protein binding / cytosol
Similarity search - Function
S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIAMINOBUTANE / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTolbert, W.D. / Zhang, Y. / Bennett, E.M. / Cottet, S.E. / Ekstrom, J.L. / Pegg, A.E. / Ealick, S.E.
Citation
Journal: Biochemistry / Year: 2003
Title: Mechanism of Human S-Adenosylmethionine Decarboxylase Proenzyme Processing as Revealed by the Structure of the S68A Mutant.
Authors: Tolbert, W.D. / Zhang, Y. / Cottet, S.E. / Bennett, E.M. / Ekstrom, J.L. / Pegg, A.E. / Ealick, S.E.
#1: Journal: Biochemistry / Year: 2001
Title: Structure of a Human S-Adenosylmethionine Decarboxylase Self-Processing Ester Intermediate and Mechanism of Putrescine Stimulation of Processing As Revealed by the H243A Mutant
Authors: Ekstrom, J.L. / Tolbert, W.D. / Xiong, H. / Pegg, A.E. / Ealick, S.E.
#2: Journal: Biochemistry / Year: 2001
Title: The Structural Basis for Substrate Specificity and Inhibition of Human S-Adenosylmethionine Decarboxylase.
Authors: Tolbert, W.D. / Ekstrom, J.L. / Mathews, I.I. / Secrist III, J.A. / Kapoor, P. / Pegg, A.E. / Ealick, S.E.
#3: Journal: Structure / Year: 1999
Title: The crystal structure of human S-adenosylmethionine decarboxylase at 2.25 A resolution reveals a novel fold.
Authors: Ekstrom, J.L. / Mathews, I.I. / Stanley, B.A. / Pegg, A.E. / Ealick, S.E.
History
DepositionSep 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine decarboxylase proenzyme
B: S-adenosylmethionine decarboxylase proenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6716
Polymers81,2502
Non-polymers4214
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint2 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.936, 56.382, 99.190
Angle α, β, γ (deg.)90.00, 110.97, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe proenzyme is a dimer and the dimer is in the asymmetric unit.

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Components

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


Mass: 40625.102 Da / Num. of mol.: 2 / Mutation: S68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pQE30 (Qiagen) / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue/JM109
References: UniProt: P17707, adenosylmethionine decarboxylase
#2: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, tris[hydroxymethyl]aminomethane, dithiothreitol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
214-16 %(w/w)PEG80001reservoir
3100 mMTris-HCl1reservoirpH8.0
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→99 Å / Num. all: 82984 / Num. obs: 76221 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.117 / Net I/σ(I): 3.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 11752 / Rsym value: 0.28 / % possible all: 96.3
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 99 Å / Num. obs: 82984 / Num. measured all: 551036 / Rmerge(I) obs: 0.117
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 96.3 % / Num. unique obs: 11752 / Num. measured obs: 41351 / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I76

1i76


Resolution: 1.75→16.37 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 7623 10 %RANDOM
Rwork0.21 ---
all0.22 76221 --
obs0.21 76221 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.1972 Å2 / ksol: 0.420892 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.91 Å20 Å2-3.44 Å2
2---0.25 Å20 Å2
3---6.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.75→16.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5428 0 28 306 5762
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.442
X-RAY DIFFRACTIONc_scbond_it3.022
X-RAY DIFFRACTIONc_scangle_it4.492.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 1227 9.9 %
Rwork0.268 11181 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEINMAOTST5.PARAMPROTEINMAOTST5.TOP
X-RAY DIFFRACTION2TRIS.PARAMTRIS.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 99 Å / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11
LS refinement shell
*PLUS
Lowest resolution: 1.76 Å / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.279

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