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- PDB-4lvq: Crystal structure of the M. tuberculosis phosphate binding protei... -

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Basic information

Entry
Database: PDB / ID: 4lvq
TitleCrystal structure of the M. tuberculosis phosphate binding protein PstS3
ComponentsPhosphate-binding protein PstS 3
KeywordsTRANSPORT PROTEIN / Phosphate binding protein / Extracellular
Function / homology
Function and homology information


biological process involved in interaction with host => GO:0051701 / symbiont-mediated suppression of host innate immune response / phosphate ion transmembrane transport / cellular response to phosphate starvation / cell wall / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / extracellular region / plasma membrane
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / PBP superfamily domain / PBP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphate-binding protein PstS 3 / Phosphate-binding protein PstS 3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFerraris, D.M. / Rizzi, M.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of the Mycobacterium tuberculosis phosphate binding protein PstS3.
Authors: Ferraris, D.M. / Spallek, R. / Oehlmann, W. / Singh, M. / Rizzi, M.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate-binding protein PstS 3
B: Phosphate-binding protein PstS 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8094
Polymers77,6192
Non-polymers1902
Water3,225179
1
A: Phosphate-binding protein PstS 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9052
Polymers38,8101
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphate-binding protein PstS 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9052
Polymers38,8101
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.207, 229.253, 39.103
Angle α, β, γ (deg.)90.00, 100.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphate-binding protein PstS 3 / PBP 3 / PstS-3 / Antigen Ag88


Mass: 38809.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pstS3, phoS2, Rv0928, MT0955, MTCY21C12.22 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A5Y2, UniProt: P9WGT7*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate, pH 6.5, 12% w/v PEG 20000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.16
ReflectionResolution: 2.3→40 Å / Num. obs: 26706 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 22.68 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.6430.274.8196.5
2.64-4030.177.3197.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.505 Å / Cor.coef. Fo:Fc: 0.816 / Cor.coef. Fo:Fc free: 0.685 / σ(F): 1.48 / Phase error: 33.18 / Stereochemistry target values: TWIN_LSQ_F / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2754 2136 8 %
Rwork0.2358 --
obs0.2389 26706 96.98 %
all-20888 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.993 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.22 Å2-0.06 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 10 179 4865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014782
X-RAY DIFFRACTIONf_angle_d1.5616512
X-RAY DIFFRACTIONf_dihedral_angle_d15.1621668
X-RAY DIFFRACTIONf_chiral_restr0.064722
X-RAY DIFFRACTIONf_plane_restr0.008876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38420.33131980.29321626X-RAY DIFFRACTION87
2.3842-2.44690.3414990.28311764X-RAY DIFFRACTION93
2.4469-2.51680.32281980.29021565X-RAY DIFFRACTION86
2.5168-2.59540.3013990.26911756X-RAY DIFFRACTION92
2.5954-2.68490.2984990.26331609X-RAY DIFFRACTION89
2.6849-2.78820.32321980.26281652X-RAY DIFFRACTION86
2.7882-2.90940.2282990.24781671X-RAY DIFFRACTION93
2.9094-3.05490.2704990.2571776X-RAY DIFFRACTION93
3.0549-3.23480.25011980.23111620X-RAY DIFFRACTION88
3.2348-3.46610.3222990.22111699X-RAY DIFFRACTION92
3.4661-3.78210.2573990.20981696X-RAY DIFFRACTION91
3.7821-4.2580.26881980.19461650X-RAY DIFFRACTION88
4.258-5.12630.2379990.19431745X-RAY DIFFRACTION92
5.1263-8.0840.24431980.25021655X-RAY DIFFRACTION88

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