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- PDB-1tmi: Structure of Thermotoga maritima S63A non-processing mutant S-ade... -

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Basic information

Entry
Database: PDB / ID: 1tmi
TitleStructure of Thermotoga maritima S63A non-processing mutant S-adenosylmethionine decarboxylase
ComponentsS-adenosylmethionine decarboxylase proenzyme, AdoMetDC, SamDC
KeywordsLYASE / two-layer alpha beta-sandwich
Function / homology
Function and homology information


adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol
Similarity search - Function
S-adenosylmethionine decarboxylase, N-terminal / S-adenosylmethionine decarboxylase, C-terminal / S-adenosylmethionine decarboxylase family, prokaryotic / S-adenosylmethionine decarboxylase proenzyme / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsToms, A.V. / Kinsland, C. / McCloskey, D.E. / Pegg, A.E. / Ealick, S.E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Evolutionary Links as Revealed by the Structure of Thermotoga maritima S-Adenosylmethionine Decarboxylase.
Authors: Toms, A.V. / Kinsland, C. / McCloskey, D.E. / Pegg, A.E. / Ealick, S.E.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine decarboxylase proenzyme, AdoMetDC, SamDC
B: S-adenosylmethionine decarboxylase proenzyme, AdoMetDC, SamDC


Theoretical massNumber of molelcules
Total (without water)29,5812
Polymers29,5812
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-14 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.968, 104.968, 69.523
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a dimer. The asymmetric unit contains 1 biological unit.

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Components

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


Mass: 14790.736 Da / Num. of mol.: 2 / Mutation: S63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: SPEH, TM0655 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)pRare
References: UniProt: Q9WZC3, adenosylmethionine decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 295.4 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium formate, HEPES, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295.4K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9792,0.9793,0.9641
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97931
30.96411
ReflectionResolution: 1.7→32.5 Å / Num. all: 31186 / Num. obs: 30984 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.048 / Net I/σ(I): 30.7
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.385 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→32.47 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 410997.27 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: twinning operator was used to ensure that pairs of twin related reflections were in the same set
RfactorNum. reflection% reflection
Rfree0.182 2954 9.4 %
Rwork0.146 --
all0.149 30984 -
obs0.146 30807 98.1 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.8139 Å2 / ksol: 0.391508 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20.32 Å20 Å2
2---1.07 Å20 Å2
3---2.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 0 148 2111
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_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.362.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.235 519 9.9 %
Rwork0.222 4263 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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