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- PDB-9lff: Crystal structure of UgpB in complex with G1P -

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Basic information

Entry
Database: PDB / ID: 9lff
TitleCrystal structure of UgpB in complex with G1P
ComponentsSN-glycerol-3-phophate ABC transporter, periplasmic SN-glycerol-3-phosphate-binding protein
KeywordsTRANSPORT PROTEIN / G1P/G3P transporter substrate-binding protein
Function / homologySN-GLYCEROL-1-PHOSPHATE / :
Function and homology information
Biological speciesPhaeobacter sp. MED193 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: SN-glycerol-3-phophate ABC transporter, periplasmic SN-glycerol-3-phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5822
Polymers49,4101
Non-polymers1721
Water7,909439
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)74.200, 114.910, 46.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SN-glycerol-3-phophate ABC transporter, periplasmic SN-glycerol-3-phosphate-binding protein


Mass: 49409.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism Phaeobacter sp. MED193 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A3X9J4.
Source: (gene. exp.) Phaeobacter sp. MED193 (bacteria) / Gene: MED193_07903 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3X9J4
#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.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M PCB buffer (pH 5.0) and 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→32.34 Å / Num. obs: 63229 / % possible obs: 99 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4198 / % possible all: 90

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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: 1.5→32.34 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 3088 4.89 %
Rwork0.1806 --
obs0.1815 63167 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 0 439 3623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063263
X-RAY DIFFRACTIONf_angle_d0.8684435
X-RAY DIFFRACTIONf_dihedral_angle_d5.256437
X-RAY DIFFRACTIONf_chiral_restr0.052467
X-RAY DIFFRACTIONf_plane_restr0.006584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.32451060.31372393X-RAY DIFFRACTION87
1.52-1.550.33031300.26732551X-RAY DIFFRACTION94
1.55-1.580.26891200.24232685X-RAY DIFFRACTION98
1.58-1.60.27471280.2272714X-RAY DIFFRACTION99
1.6-1.630.24281410.22212712X-RAY DIFFRACTION99
1.63-1.670.28071410.2252698X-RAY DIFFRACTION99
1.67-1.70.23191490.22022715X-RAY DIFFRACTION100
1.7-1.740.24881410.21062724X-RAY DIFFRACTION100
1.74-1.790.25031450.21372723X-RAY DIFFRACTION100
1.79-1.840.22691300.20032739X-RAY DIFFRACTION100
1.84-1.890.22371440.20122734X-RAY DIFFRACTION100
1.89-1.950.20531600.1942723X-RAY DIFFRACTION100
1.95-2.020.23051340.19462746X-RAY DIFFRACTION100
2.02-2.10.20641390.19012764X-RAY DIFFRACTION100
2.1-2.20.21521380.1842764X-RAY DIFFRACTION100
2.2-2.310.19231510.17892738X-RAY DIFFRACTION100
2.31-2.460.20641290.17912777X-RAY DIFFRACTION100
2.46-2.650.19691480.17562785X-RAY DIFFRACTION100
2.65-2.910.1991590.17412774X-RAY DIFFRACTION100
2.91-3.330.16051540.16242802X-RAY DIFFRACTION100
3.33-4.20.16431500.14632840X-RAY DIFFRACTION100
4.2-32.340.17321510.16112978X-RAY DIFFRACTION100

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