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- PDB-1lc8: Crystal Structure of L-Threonine-O-3-phosphate Decarboxylase from... -

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Basic information

Entry
Database: PDB / ID: 1lc8
TitleCrystal Structure of L-Threonine-O-3-phosphate Decarboxylase from S. enterica complexed with its reaction intermediate
ComponentsL-Threonine-O-3-Phosphate Decarboxylase
KeywordsLYASE / CobD / L-threonine-O-3-phosphate / PLP-dependent decarboxylase / cobalamin
Function / homology
Function and homology information


threonine-phosphate decarboxylase / threonine-phosphate decarboxylase activity / cobalamin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding
Similarity search - Function
L-threonine-O-3-phosphate decarboxylase / 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 ...L-threonine-O-3-phosphate decarboxylase / 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
Chem-33P / Threonine-phosphate decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCheong, C.-G. / Escalante-Semerena, J. / Rayment, I.
CitationJournal: Biochemistry / Year: 2002
Title: Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes.
Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionApr 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE According to the authors, the GenBank entry is in error because the original DNA sequence ... SEQUENCE According to the authors, the GenBank entry is in error because the original DNA sequence had some errors. The electron density also supports it. The new sequence is Gln25, Ser30, Val42, Arg44 and Ala45. Arg44 lacks side chain density. The organism name in this GenBank entry is Salmonella typhimurium. Salmonella typhimurium has been changed to Salmonella enterica. Therefore, the two names are same.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-Threonine-O-3-Phosphate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2362
Polymers40,8501
Non-polymers3861
Water4,882271
1
A: L-Threonine-O-3-Phosphate Decarboxylase
hetero molecules

A: L-Threonine-O-3-Phosphate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4724
Polymers81,7002
Non-polymers7722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area5660 Å2
ΔGint-34 kcal/mol
Surface area26090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.646, 103.293, 117.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222
Detailsthe second subunit of biological dimer can be generated by the operation of crystallographic two-fold symmetry axis

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Components

#1: Protein L-Threonine-O-3-Phosphate Decarboxylase / CobD


Mass: 40849.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: cobD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(JE4094) / References: UniProt: P97084
#2: Chemical ChemComp-33P / {3-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-PROPYL}-PHOSPHONIC ACID


Mass: 386.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N2O9P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 298 K / pH: 6
Details: PEG methyl ether 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 mML-threonine phosphate11
28 mg/mlprotein11
34 %PEG2000ME11
4150 mM11NaCl
5100 mMMES11pH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9763 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→500 Å / Num. obs: 37471 / % possible obs: 99.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 31.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 5.8 / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 500 Å / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.331

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KUS

1kus
PDB Unreleased entry


Resolution: 1.8→500 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1862 5 %random
Rwork0.196 ---
obs-37471 --
Refinement stepCycle: LAST / Resolution: 1.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 24 271 3030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.57
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 500 Å / Num. reflection obs: 35608 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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