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- PDB-4hah: Structure of the Salmonella plasmid virulence C protein (SpvC) -

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Basic information

Entry
Database: PDB / ID: 4hah
TitleStructure of the Salmonella plasmid virulence C protein (SpvC)
Components27.5 kDa virulence protein
KeywordsLYASE / Phosphothreonine Lyase
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 enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShenoy, A.G. / Johnson, S.J. / Hengge, A.C.
CitationJournal: To be Published
Title: Mechanistic and structural investigations of phosphothreonine lyase class of enzymes.
Authors: Vyacheslav, I.K. / Shenoy, A.G. / Johnson, S.J. / Hengge, A.C.
History
DepositionSep 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: 27.5 kDa virulence protein
B: 27.5 kDa virulence protein


Theoretical massNumber of molelcules
Total (without water)55,3622
Polymers55,3622
Non-polymers00
Water8,431468
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 area2360 Å2
ΔGint-12 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.528, 71.912, 106.490
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


Mass: 27681.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: mkaD, PSLT038, SPV, spvC, vsdD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (RIL) / References: UniProt: P0A2M9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 44.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350 (a 50% w/v solution) 0.1M Ammonium Chloride (1M stock solution) , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2011 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→32.264 Å / Num. all: 331429 / Num. obs: 45887 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.22 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.35 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4573 / % possible all: 86.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.264 Å / SU ML: 0.59 / σ(F): 0 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1988 4.36 %random
Rwork0.1935 ---
obs0.1952 45609 97.83 %-
all-47397 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.385 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4282 Å20 Å20 Å2
2--0.8316 Å2-0 Å2
3---5.6137 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 0 468 3964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073580
X-RAY DIFFRACTIONf_angle_d1.0244814
X-RAY DIFFRACTIONf_dihedral_angle_d14.2711362
X-RAY DIFFRACTIONf_chiral_restr0.069482
X-RAY DIFFRACTIONf_plane_restr0.004646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8-1.86430.35871690.33123726372685
1.8643-1.9390.29381950.28244232423296
1.939-2.02720.30121970.23784366436699
2.0272-2.13410.27462000.20984370437099
2.1341-2.26770.22862010.18834402440299
2.2677-2.44280.22882000.183844084408100
2.4428-2.68850.2692030.19344474447100
2.6885-3.07730.23932030.192144594459100
3.0773-3.8760.20942060.172145284528100
3.876-32.26910.18522140.171346834683100

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