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- PDB-2z8p: Structural basis for the catalytic mechanism of phosphothreonine lyase -

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Basic information

Entry
Database: PDB / ID: 2z8p
TitleStructural basis for the catalytic mechanism of phosphothreonine lyase
Components
  • (GLY)(GLU)(ALA)(TPO)(VAL)(PTR)(ALA)
  • 27.5 kDa virulence protein
KeywordsLYASE / short three-helix bundle / distorted beta-strand sheet
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / extracellular region
Similarity search - Function
Phosphothreonine lyase fold / phosphothreonine lyase / OspF/SpvC / OspF/SpvC superfamily / Salmonella virulence-associated 28kDa protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MAPK phosphothreonine lyase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, L. / Wang, H. / Gu, L. / Huang, N. / Zhou, J.M. / Chai, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for the catalytic mechanism of phosphothreonine lyase.
Authors: Chen, L. / Wang, H. / Zhang, J. / Gu, L. / Huang, N. / Zhou, J.M. / Chai, J.
History
DepositionSep 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 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
A: 27.5 kDa virulence protein
B: (GLY)(GLU)(ALA)(TPO)(VAL)(PTR)(ALA)


Theoretical massNumber of molelcules
Total (without water)28,4932
Polymers28,4932
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.310, 71.420, 98.960
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 27.5 kDa virulence protein / Spvc / phosphothreonine lyase


Mass: 27623.037 Da / Num. of mol.: 1 / Mutation: K136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pGEX6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A2M9
#2: Protein/peptide (GLY)(GLU)(ALA)(TPO)(VAL)(PTR)(ALA)


Mass: 869.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG (MME) 2000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 22, 2007
RadiationMonochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→99 Å / Num. all: 25249 / Num. obs: 25173 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 47.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 8.5 / % possible all: 99.7

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Processing

Software
NameClassification
MAR345dtbdata collection
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z8O

2z8o


Resolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.229 --RANDOM
Rwork0.211 ---
all-25249 --
obs-25173 99.7 %-
Displacement parametersBiso mean: 34.9473 Å2
Baniso -1Baniso -2Baniso -3
1-3.516 Å20 Å20 Å2
2--0.581 Å20 Å2
3----4.097 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 0 259 2078
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.006
X-RAY DIFFRACTIONr_angle_refined_deg1.35
LS refinement shellResolution: 1.8→1.82 Å
RfactorNum. reflection% reflection
Rfree0.303 42 -
Rwork0.267 --
obs-943 97.7 %

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