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- PDB-5ihf: Salmonella Typhimurium VirG-like (STV) protein -

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Basic information

Entry
Database: PDB / ID: 5ihf
TitleSalmonella Typhimurium VirG-like (STV) protein
ComponentsVirG-like protein
KeywordsUNKNOWN FUNCTION / LTxxQ motif / CpxP_like family
Function / homologyLTXXQ motif family protein / LTXXQ motif family protein / periplasmic space / PHOSPHATE ION / VirG-like protein / Probable secreted protein (SPI-6 associated)
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.576 Å
AuthorsPandey, N.K. / Ray, S. / Suar, M. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: To Be Published
Title: Salmonella Typhimurium VirG-like (STV) protein
Authors: Pandey, N.K. / Ray, S. / Suar, M. / Bhavesh, N.S.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
A: VirG-like protein
B: VirG-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8988
Polymers26,4002
Non-polymers4986
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-56 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.960, 59.710, 63.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein VirG-like protein


Mass: 13200.012 Da / Num. of mol.: 2 / Fragment: UNP residues 24-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Strain: SL1344 / Gene: SL1344_RS01575 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6AXB3, UniProt: A0A0H3ND95*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.8 M Sodium Phosphate Monobasic Monohydrate, Potassium Phosphate Dibasic
PH range: 4.8-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7712 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.576→63.13 Å / Num. obs: 30511 / % possible obs: 97.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.52 Å2 / Rsym value: 0.069 / Net I/av σ(I): 3.969 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.58-1.663.60.681.2198.5
1.66-1.763.80.4331.8199.3
1.76-1.883.80.2393.3199.1
1.88-2.033.80.1245.9198.5
2.03-2.233.90.0797.8198.3
2.23-2.493.90.0639.3197.6
2.49-2.883.90.0629.1196.7
2.88-3.523.90.077.7196.2
3.52-4.983.90.0668.2194.6
4.98-43.383.60.05210.5183.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.58 Å43.38 Å
Translation1.58 Å43.38 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
SCALA3.3.21data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IO8

5io8


Resolution: 1.576→43.38 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.213 1363 4.47 %
Rwork0.203 --
obs0.2035 30461 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.57 Å2 / Biso mean: 44.7161 Å2 / Biso min: 19.32 Å2
Refinement stepCycle: final / Resolution: 1.576→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 26 185 1862
Biso mean--92.84 47.21 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041707
X-RAY DIFFRACTIONf_angle_d0.7852330
X-RAY DIFFRACTIONf_chiral_restr0.03270
X-RAY DIFFRACTIONf_plane_restr0.003301
X-RAY DIFFRACTIONf_dihedral_angle_d13.808622
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.576-1.63230.34641150.28222887300298
1.6323-1.69770.2954860.26492999308599
1.6977-1.7750.275950.25412960305599
1.775-1.86850.30751260.24422940306699
1.8685-1.98560.24991930.22212862305598
1.9856-2.13890.22881510.1972916306798
2.1389-2.35420.19611400.19082905304597
2.3542-2.69480.19971760.20122891306797
2.6948-3.39490.22691310.19812906303795
3.3949-43.39640.19061500.19252832298289

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