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- PDB-7xg8: Crystal structure of PstS protein from cyanophage P-SSM2 -

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Basic information

Entry
Database: PDB / ID: 7xg8
TitleCrystal structure of PstS protein from cyanophage P-SSM2
ComponentsABC transporter, substrate binding protein, phosphate
KeywordsTRANSPORT PROTEIN / phosphate binding protein / cyanobacteria / cyanophage
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 / PHOSPHATE ION / ABC transporter, substrate binding protein, phosphate
Function and homology information
Biological speciesProchlorococcus phage P-SSM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCai, K. / Jiang, Y.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Environ.Microbiol. / Year: 2022
Title: Biochemical and structural characterization of the cyanophage-encoded phosphate-binding protein: implications for enhanced phosphate uptake of infected cyanobacteria
Authors: Zhao, F. / Lin, X. / Cai, K. / Jiang, Y. / Ni, T. / Chen, Y. / Feng, J. / Dang, S. / Zhou, C.Z. / Zeng, Q.
History
DepositionApr 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, substrate binding protein, phosphate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9142
Polymers33,8191
Non-polymers951
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-9 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.774, 63.525, 108.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter, substrate binding protein, phosphate / Phosphate transporter subunit


Mass: 33819.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus phage P-SSM2 (virus) / Gene: pstS, PCMG_00251, PSSM2_248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58MA7
#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.: 26 / 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: 37.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) polyethylene glycol 3350, 0.1 M citric acid, pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 13262 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 17.965
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 8.132 / Num. unique obs: 1287 / Rsym value: 0.37 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2abh

2abh


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.859 / SU B: 7.451 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.279 616 4.7 %RANDOM
Rwork0.227 ---
obs0.2293 12606 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.4 Å2 / Biso mean: 20.523 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å2-0 Å2
2---0.89 Å20 Å2
3---1.07 Å2
Refinement stepCycle: final / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 5 26 2248
Biso mean--17.81 15.89 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022264
X-RAY DIFFRACTIONr_bond_other_d0.0020.022165
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9573065
X-RAY DIFFRACTIONr_angle_other_deg0.99234985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28624.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40615373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0331512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212619
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02503
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.279 36 -
Rwork0.244 901 -
obs--98.22 %

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