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- PDB-9lb6: Crystal structure of trehalose 6-phosphate phosphatase Weissella ceti -

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Basic information

Entry
Database: PDB / ID: 9lb6
TitleCrystal structure of trehalose 6-phosphate phosphatase Weissella ceti
ComponentsTrehalose-6-phosphate hydrolase
KeywordsHYDROLASE / trehalose 6-phosphate phosphatase
Function / homology
Function and homology information


glycosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase / Glycoside hydrolase, family 65, central catalytic / Glycoside hydrolase, family 65, N-terminal / Glycosyl hydrolase family 65 central catalytic domain / Glycosyl hydrolase family 65, N-terminal domain / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Trehalose-6-phosphate hydrolase
Similarity search - Component
Biological speciesWeissella ceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsFeng, Y. / Xue, S.
Funding support China, 1items
OrganizationGrant numberCountry
Other privateDUT24LAB104 China
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Structural Insights into Trehalose-6-Phosphate Phosphorylase and Its Role in Trehalose 6-Phosphate Biosynthesis via a Multienzyme Cascade.
Authors: Feng, Y. / Wang, N. / Cao, Q. / Li, S. / Xu, Y. / Che, X. / Zhao, J. / Yang, C. / Xue, S.
History
DepositionJan 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trehalose-6-phosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8402
Polymers86,6451
Non-polymers1941
Water15,385854
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)179.541, 61.695, 77.048
Angle α, β, γ (deg.)90.000, 105.820, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1412-

HOH

21A-1754-

HOH

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Components

#1: Protein Trehalose-6-phosphate hydrolase


Mass: 86645.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: trehalose 6-phosphate phosphatase / Source: (gene. exp.) Weissella ceti (bacteria) / Gene: WS74_1295 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075U1V9
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate (pH 6.5), and 18% (w/v) polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.91→43.18 Å / Num. obs: 62370 / % possible obs: 98.13 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.29 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rsym value: 0.1789 / Net I/σ(I): 8.65
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.33 / Num. unique obs: 5457 / CC1/2: 0.824 / CC star: 0.95 / Rsym value: 0.5494 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
HKL-2000v722-Linuxdata reduction
HKL-2000v722-Linuxdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→43.18 Å / SU ML: 0.1579 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.1368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1813 2885 5.12 %
Rwork0.1507 53440 -
obs0.1523 56324 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.32 Å2
Refinement stepCycle: LAST / Resolution: 1.98→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 13 854 6957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666231
X-RAY DIFFRACTIONf_angle_d0.84228482
X-RAY DIFFRACTIONf_chiral_restr0.0568952
X-RAY DIFFRACTIONf_plane_restr0.00671109
X-RAY DIFFRACTIONf_dihedral_angle_d6.4055845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.010.25241360.19062424X-RAY DIFFRACTION96.42
2.01-2.050.22221120.17022495X-RAY DIFFRACTION98.12
2.05-2.080.18911260.16272526X-RAY DIFFRACTION98.62
2.08-2.120.19151370.15712509X-RAY DIFFRACTION98.88
2.12-2.170.19691430.15142521X-RAY DIFFRACTION99.33
2.17-2.210.1991370.15812531X-RAY DIFFRACTION99.44
2.22-2.270.18761530.15762522X-RAY DIFFRACTION99.55
2.27-2.320.20681350.15422540X-RAY DIFFRACTION99.55
2.32-2.390.20671180.15012554X-RAY DIFFRACTION99.63
2.39-2.460.17671300.15522560X-RAY DIFFRACTION99.81
2.46-2.540.19731470.15132550X-RAY DIFFRACTION99.85
2.54-2.630.20011460.15432528X-RAY DIFFRACTION99.74
2.63-2.730.18831320.15352550X-RAY DIFFRACTION99.7
2.73-2.860.20561370.1592589X-RAY DIFFRACTION100
2.86-3.010.18011470.15952523X-RAY DIFFRACTION100
3.01-3.190.20291290.15922594X-RAY DIFFRACTION100
3.19-3.440.18861430.15052550X-RAY DIFFRACTION99.81
3.44-3.790.15141430.14242588X-RAY DIFFRACTION99.78
3.79-4.330.14891460.12562552X-RAY DIFFRACTION99.89
4.33-5.460.14231430.12972601X-RAY DIFFRACTION99.85
5.46-43.180.17491440.15972633X-RAY DIFFRACTION98.72

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