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- PDB-9u8e: Crystal structure of Leminorella grimontii GatC in the presence o... -

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Basic information

Entry
Database: PDB / ID: 9u8e
TitleCrystal structure of Leminorella grimontii GatC in the presence of D-xylose
ComponentsPTS galactitol transporter subunit IIC
KeywordsTRANSPORT PROTEIN / PTS / xylose / transporter
Function / homology
Function and homology information


galactitol transmembrane transporter activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / plasma membrane
Similarity search - Function
Galactitol permease IIC component / Phosphotransferase system, sugar-specific permease component / PTS system sugar-specific permease component / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile.
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PTS galactitol transporter subunit IIC
Similarity search - Component
Biological speciesLeminorella grimontii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTakahashi, Y.S. / Kohga, H. / Yamamoto, K. / Takahashi, J.F. / Tanaka, Y. / Ichikawa, M. / Miyazaki, R. / Tsukazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural basis of a phosphotransferase system xylose transporter
Authors: Takahashi, Y.S. / Kohga, H. / Chek, M.F. / Yamamoto, K. / Takahashi, J.F. / Shigematsu, H. / Tanaka, H. / Ichikawa, M. / Miyazaki, R. / Hakoshima, T. / Tsukazaki, T.
History
DepositionMar 26, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS galactitol transporter subunit IIC
B: PTS galactitol transporter subunit IIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2958
Polymers100,1562
Non-polymers2,1396
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-33 kcal/mol
Surface area35700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.760, 100.610, 122.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein PTS galactitol transporter subunit IIC


Mass: 50078.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leminorella grimontii (bacteria) / Gene: SOASR030_34840 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAV5N9B3
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
Has ligand of interestN
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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 8
Details: 100mM Na-acetate, 100mM Tris-HCl (pH8.0), 40-45% PEG 200, 10mM D-xylose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→46.53 Å / Num. obs: 16782 / % possible obs: 98.98 % / Redundancy: 93.4 % / CC1/2: 0.934 / Net I/σ(I): 4.98
Reflection shellResolution: 3.3→3.4 Å / Num. unique obs: 3396 / CC1/2: 0.413

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→46.53 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 1677 9.99 %
Rwork0.2223 --
obs0.2278 16782 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 104 0 6812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.521
X-RAY DIFFRACTIONf_dihedral_angle_d4.5731016
X-RAY DIFFRACTIONf_chiral_restr0.0391154
X-RAY DIFFRACTIONf_plane_restr0.0071148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.40.34251370.26911235X-RAY DIFFRACTION100
3.4-3.510.34331390.24011255X-RAY DIFFRACTION100
3.51-3.630.27941370.23211235X-RAY DIFFRACTION100
3.63-3.780.30981390.23141245X-RAY DIFFRACTION100
3.78-3.950.27251390.20761243X-RAY DIFFRACTION100
3.95-4.160.25021390.20341253X-RAY DIFFRACTION100
4.16-4.420.28731390.21841256X-RAY DIFFRACTION100
4.42-4.760.33061320.26411196X-RAY DIFFRACTION95
4.76-5.240.24771400.21291263X-RAY DIFFRACTION100
5.24-5.990.28771420.23611274X-RAY DIFFRACTION100
5.99-7.540.24331450.21571302X-RAY DIFFRACTION100
7.55-46.530.22741490.18761348X-RAY DIFFRACTION98

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