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- PDB-9jwy: Crystal structure of PstS from Candidatus Pelagibacter sp. HTCC72... -

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Basic information

Entry
Database: PDB / ID: 9jwy
TitleCrystal structure of PstS from Candidatus Pelagibacter sp. HTCC7211 in complex with phosphate
ComponentsPhosphate ABC transporter, periplasmic phosphate-binding protein
KeywordsPROTEIN BINDING / Transporter / Complex / Phosphate / PstS / TRANSPORT PROTEIN
Function / homologyphosphate-transporting ATPase / : / PBP domain / PBP superfamily domain / hydrolase activity / PHOSPHATE ION / Phosphate ABC transporter, periplasmic phosphate-binding protein
Function and homology information
Biological speciesCandidatus Pelagibacter sp. HTCC7211 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhu, W.J. / Wang, P. / Cao, H.Y. / Zhang, Y.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32170127, 32370136 China
CitationJournal: Mbio / Year: 2025
Title: Structural and molecular basis for phosphate recognition by SAR11 bacteria.
Authors: Zhu, W.J. / Wang, C. / Liu, L. / Li, J.X. / Wang, H.Q. / Wang, M.Q. / Cao, H.Y. / Chen, X.L. / Qin, Q.L. / Zhang, Y.Z. / Sun, M.L. / Wang, P.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 3, 2025Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 24, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate ABC transporter, periplasmic phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8662
Polymers36,7711
Non-polymers951
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.270, 46.870, 82.990
Angle α, β, γ (deg.)90.00, 102.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphate ABC transporter, periplasmic phosphate-binding protein


Mass: 36770.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Pelagibacter sp. HTCC7211 (bacteria)
Gene: pstS, PB7211_1190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6BPR5, phosphate-transporting ATPase
#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.: 313 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium Chloride, 0.1 M Tris (pH 8.0), 24% (w/v) polyethylene glycol (PEG) 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→46.87 Å / Num. obs: 101152 / % possible obs: 95.5 % / Redundancy: 5.4 % / CC1/2: 0.99 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 18666 / CC1/2: 0.976

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JWO

4jwo


Resolution: 2→40.55 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 3481 9.89 %
Rwork0.172 --
obs0.1771 85732 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 5 314 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072381
X-RAY DIFFRACTIONf_angle_d0.8993212
X-RAY DIFFRACTIONf_dihedral_angle_d6.354324
X-RAY DIFFRACTIONf_chiral_restr0.055356
X-RAY DIFFRACTIONf_plane_restr0.006408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.26931460.18441276X-RAY DIFFRACTION91
2.03-2.060.28371140.20491109X-RAY DIFFRACTION85
2.06-2.090.28931380.1991268X-RAY DIFFRACTION90
2.09-2.120.24121450.18191297X-RAY DIFFRACTION94
2.12-2.150.25491370.17221298X-RAY DIFFRACTION95
2.15-2.190.24851420.17491281X-RAY DIFFRACTION95
2.19-2.230.24191500.17691335X-RAY DIFFRACTION95
2.23-2.270.26381440.19661275X-RAY DIFFRACTION95
2.27-2.320.30871320.17771264X-RAY DIFFRACTION94
2.32-2.370.25531470.1751294X-RAY DIFFRACTION94
2.37-2.430.24051440.17431278X-RAY DIFFRACTION93
2.43-2.490.23831240.18021145X-RAY DIFFRACTION85
2.49-2.550.27621410.17391272X-RAY DIFFRACTION91
2.55-2.630.2821400.17681323X-RAY DIFFRACTION97
2.63-2.710.24241350.19151300X-RAY DIFFRACTION95
2.71-2.810.24881470.1881293X-RAY DIFFRACTION95
2.81-2.920.25351450.19191297X-RAY DIFFRACTION94
2.92-3.060.22131430.18091274X-RAY DIFFRACTION95
3.06-3.220.21761260.17371219X-RAY DIFFRACTION88
3.22-3.420.1951450.16391261X-RAY DIFFRACTION93
3.42-3.680.18381490.1571315X-RAY DIFFRACTION97
3.68-4.050.1831360.14611308X-RAY DIFFRACTION95
4.05-4.640.17991370.1411235X-RAY DIFFRACTION89
4.64-5.840.16051430.15671230X-RAY DIFFRACTION91
5.84-40.550.19751310.1811285X-RAY DIFFRACTION93

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