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- PDB-8ods: Phosphate-Binding Protein (PstS) from Xanthomonas citri pv. citri... -

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Basic information

Entry
Database: PDB / ID: 8ods
TitlePhosphate-Binding Protein (PstS) from Xanthomonas citri pv. citri A306 bound to phosphate
ComponentsPhosphate-binding protein PstS
KeywordsTRANSPORT PROTEIN / SBP / Pho Regulon / ABC transporter
Function / homologyPhosphate ABC transporter, substrate-binding protein PstS / PBP domain / PBP superfamily domain / phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex / Prokaryotic membrane lipoprotein lipid attachment site profile. / PHOSPHATE ION / Phosphate-binding protein PstS
Function and homology information
Biological speciesXanthomonas citri pv. citri str. 306 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.909 Å
AuthorsSantos, L.S. / Balan, A. / Guskov, A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2020/10171-0 Brazil
CitationJournal: To Be Published
Title: Phosphate-Binding Protein (PstS) from Xanthomonas citri pv. citri A306
Authors: Santos, L.S. / Balan, A. / Guskov, A.
History
DepositionMar 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2392
Polymers36,1441
Non-polymers951
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-8 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.37, 73.137, 99.165
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphate-binding protein PstS


Mass: 36144.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri pv. citri str. 306 (bacteria)
Strain: A306 / Gene: pstS / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PM56
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-HCl (pH 8.0), 50 mM KCl, 20% PEG 6000, 20 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.909→41.04 Å / Num. obs: 24939 / % possible obs: 97.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 18.53 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.09772 / Rpim(I) all: 0.03365 / Rrim(I) all: 0.1001 / Net I/σ(I): 14.73
Reflection shellResolution: 1.909→1.977 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.01 / Num. unique obs: 2201 / CC1/2: 0.921 / CC star: 0.979 / Rpim(I) all: 0.2064 / Rrim(I) all: 0.4674 / % possible all: 87.58

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSJan 10, 2022data reduction
XSCALEJan 10, 2022data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.909→41.04 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.157
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 1237 -RANDOM
Rwork0.2048 ---
obs0.2071 24728 98 %-
Displacement parametersBiso mean: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1-3.093 Å20 Å20 Å2
2---4.7649 Å20 Å2
3---1.6719 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.909→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 5 301 2640
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082408HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.983282HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d783SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes413HARMONIC5
X-RAY DIFFRACTIONt_it2408HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion311SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2604SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion16.97
LS refinement shellResolution: 1.91→1.93 Å
RfactorNum. reflection% reflection
Rfree0.649 25 -
Rwork0.3979 --
obs0.41 495 70.58 %

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