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- PDB-9lf9: Crystal structure of GpxB in complex with G1P -

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Basic information

Entry
Database: PDB / ID: 9lf9
TitleCrystal structure of GpxB in complex with G1P
ComponentsPhosphonate ABC transporter, periplasmic phosphonate-binding protein
KeywordsTRANSPORT PROTEIN / G1P/G3P transporter substrate-binding protein
Function / homologyPhosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / SN-GLYCEROL-1-PHOSPHATE / Phosphonate ABC transporter, periplasmic phosphonate-binding protein
Function and homology information
Biological speciesMarinobacter sp. DSM 11874 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsWang, N. / Li, C.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural basis and evolutionary pathways of glycerol-1-phosphate transport in marine bacteria.
Authors: Wang, N. / Westermann, L.M. / Li, M. / Li, C. / Murphy, A. / Gu, Z. / Silvano, E. / Blindauer, C.A. / Lidbury, I.D. / Zhang, Y. / Scanlan, D.J. / Chen, Y.
History
DepositionJan 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4472
Polymers35,2751
Non-polymers1721
Water6,774376
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)136.280, 136.280, 136.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Phosphonate ABC transporter, periplasmic phosphonate-binding protein


Mass: 35275.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism "Marinobacter sp. DSM 11874" is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A1U5Q9.
Source: (gene. exp.) Marinobacter sp. DSM 11874 (bacteria) / Gene: Maqu_3257 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1U5Q9
#2: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: potassium phosphate, polyethylene glycol (PEG) 8000 and glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.68→30.47 Å / Num. obs: 47905 / % possible obs: 100 % / Redundancy: 31.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 22
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.22 / Num. unique obs: 3543 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→30.47 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 2392 4.99 %
Rwork0.1532 --
obs0.154 47895 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 0 376 2666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.894
X-RAY DIFFRACTIONf_dihedral_angle_d5.916315
X-RAY DIFFRACTIONf_chiral_restr0.062342
X-RAY DIFFRACTIONf_plane_restr0.006424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.29051040.26062702X-RAY DIFFRACTION100
1.71-1.750.25631490.22872673X-RAY DIFFRACTION100
1.75-1.790.22211340.19652639X-RAY DIFFRACTION100
1.79-1.840.18691440.1752644X-RAY DIFFRACTION100
1.84-1.890.18651360.16682649X-RAY DIFFRACTION100
1.89-1.940.16211590.15432641X-RAY DIFFRACTION100
1.94-20.16541530.14882673X-RAY DIFFRACTION100
2.01-2.080.17691330.15722649X-RAY DIFFRACTION100
2.08-2.160.15091570.15642651X-RAY DIFFRACTION100
2.16-2.260.17431470.14782648X-RAY DIFFRACTION100
2.26-2.380.19721340.15622682X-RAY DIFFRACTION100
2.38-2.530.18751400.1522668X-RAY DIFFRACTION100
2.53-2.720.17341380.16412700X-RAY DIFFRACTION100
2.72-2.990.17061560.15522645X-RAY DIFFRACTION100
3-3.430.16281320.14672724X-RAY DIFFRACTION100
3.43-4.310.14891270.1292728X-RAY DIFFRACTION100
4.32-30.470.14841490.14732787X-RAY DIFFRACTION100

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