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- PDB-2p1w: structure of the phosphothreonine lyase SpvC, the effector protei... -

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Basic information

Entry
Database: PDB / ID: 2p1w
Titlestructure of the phosphothreonine lyase SpvC, the effector protein from Salmonella
Components27.5 kDa virulence protein
KeywordsLYASE / beta sheet- alpha helix
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 enteritidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhu, Y. / Wang, D.C. / Shao, F.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase.
Authors: Zhu, Y. / Li, H. / Long, C. / Hu, L. / Xu, H. / Liu, L. / Chen, S. / Wang, D.C. / Shao, F.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 27.5 kDa virulence protein


Theoretical massNumber of molelcules
Total (without water)28,8761
Polymers28,8761
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.352, 70.352, 101.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

#1: Protein 27.5 kDa virulence protein / SpvC / phosphothreonine lyase


Mass: 28876.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enteritidis (bacteria) / Gene: SpvC / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P0A2N1, Lyases; Carbon-oxygen lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG3350, 0.1M TrisHCl pH8.0, 5% Tacsimate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9794 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 15486 / Num. obs: 15052 / % possible obs: 97.2 % / Redundancy: 27.3 % / Rmerge(I) obs: 0.098 / Rsym value: 0.08 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 23.5 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 30 / Num. unique all: 1806 / Rsym value: 0.378 / % possible all: 72.2

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se24.3650.1440.2930.8051.336
2Se28.6190.0080.4260.8421.374
3Se23.2950.1450.7040.2751.144
4Se20.2560.1860.7570.2221.067
5Se54.9110.050.2710.4231.429
6Se37.1980.0610.6150.9480.811
7Se600.0550.0940.4351.445
Phasing dmFOM : 0.63 / FOM acentric: 0.64 / FOM centric: 0.59 / Reflection: 13546 / Reflection acentric: 11435 / Reflection centric: 2111
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.1-35.1360.830.90.72740450290
3.8-6.10.870.910.7420421587455
3-3.80.810.830.7124582056402
2.6-30.660.680.5524412106335
2.3-2.60.490.50.438933473420
2.1-2.30.360.360.3519721763209

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Processing

Software
NameVersionClassificationNB
SOLVE2.12phasing
RESOLVE2.12phasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.229 590 5 %
Rwork0.191 --
obs-11678 98.5 %
Solvent computationBsol: 30.949 Å2
Displacement parametersBiso mean: 25.698 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2---2.29 Å20 Å2
3---4.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 0 180 1843
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4241.5
X-RAY DIFFRACTIONc_scbond_it2.4312
X-RAY DIFFRACTIONc_mcangle_it2.3332
X-RAY DIFFRACTIONc_scangle_it3.4892.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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