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- PDB-2z8m: Structural basis for the catalytic mechanism of phosphothreonine lyase -

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Basic information

Entry
Database: PDB / ID: 2z8m
TitleStructural basis for the catalytic mechanism of phosphothreonine lyase
Components27.5 kDa virulence protein
KeywordsLYASE / short three-helix bundle / distorted beta-strand sheet / Virulence
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: 2 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 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 27.5 kDa virulence protein
B: 27.5 kDa virulence protein


Theoretical massNumber of molelcules
Total (without water)55,3622
Polymers55,3622
Non-polymers00
Water7,476415
1
A: 27.5 kDa virulence protein


Theoretical massNumber of molelcules
Total (without water)27,6811
Polymers27,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 27.5 kDa virulence protein


Theoretical massNumber of molelcules
Total (without water)27,6811
Polymers27,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.490, 71.950, 106.270
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: 27681.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: mkaD, spvC, vsdD / Plasmid: PGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A2M9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 4000, 100mM HEPES, pH 7.0, 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: Dec 16, 2006
RadiationMonochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 34077 / Num. obs: 32847 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 36.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 7.9 / % possible all: 94.7

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Processing

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

2z8o


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 --RANDOM
Rwork0.205 ---
all-34077 --
obs-32847 96.4 %-
Displacement parametersBiso mean: 39.7586 Å2
Baniso -1Baniso -2Baniso -3
1-1.323 Å20 Å20 Å2
2--2.455 Å20 Å2
3----3.778 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 0 415 3911
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.006
X-RAY DIFFRACTIONr_angle_refined_deg1.21
LS refinement shellResolution: 2→2.02 Å
RfactorNum. reflection% reflection
Rfree0.353 37 -
Rwork0.218 --
obs-1004 94.7 %

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