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- PDB-1tlu: Crystal Structure of Thermotoga maritima S-adenosylmethionine dec... -

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Basic information

Entry
Database: PDB / ID: 1tlu
TitleCrystal Structure of Thermotoga maritima 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 / SINGLE WAVELENGTH / Resolution: 1.55 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 9, 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 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,6132
Polymers29,6132
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-16 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.994, 104.994, 69.695
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: 14806.736 Da / Num. of mol.: 2
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): B834(DE3)
References: UniProt: Q9WZC3, adenosylmethionine decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 52 %
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: 0.9786 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.55→24.47 Å / Num. all: 40567 / Num. obs: 39077 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.04 / Net I/σ(I): 29.3
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.339 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SINGLE WAVELENGTH / Resolution: 1.55→24.47 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 630823.03 / 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
Rfree0.187 3788 9.1 %
Rwork0.152 --
all0.155 40567 -
obs0.155 39077 93.9 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.5213 Å2 / ksol: 0.436414 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20.42 Å20 Å2
2---0.65 Å20 Å2
3---1.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.55→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 0 162 2100
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 1.55→1.67 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.262 685 8.3 %
Rwork0.254 6387 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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