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- PDB-9lb7: Crystal structure of trehalose-6-phosphate phosphorylase from Wei... -

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Basic information

Entry
Database: PDB / ID: 9lb7
TitleCrystal structure of trehalose-6-phosphate phosphorylase from Weissella ceti in complex with beta-Glc1P
ComponentsTrehalose-6-phosphate hydrolase
KeywordsHYDROLASE / trehalose-6-phosphate phosphorylase
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
1-O-phosphono-beta-D-glucopyranose / Trehalose-6-phosphate hydrolase
Similarity search - Component
Biological speciesWeissella ceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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

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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)86,9303
Polymers86,6451
Non-polymers2842
Water5,963331
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)181.376, 62.165, 77.265
Angle α, β, γ (deg.)90.000, 106.090, 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

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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
Source: (gene. exp.) Weissella ceti (bacteria) / Gene: WS74_1295 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075U1V9
#2: Sugar ChemComp-XGP / 1-O-phosphono-beta-D-glucopyranose / 1-O-phosphono-beta-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
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 PILATUS 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: 2.35→48.21 Å / Num. obs: 34466 / % possible obs: 99.97 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.53 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.195 / Net I/σ(I): 10.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1710 / CC1/2: 0.816 / % possible all: 88.01

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
HKL-2000v722data reduction
HKL-2000v722data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→48.21 Å / SU ML: 0.3122 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.255 1716 4.95 %
Rwork0.224 30572 -
obs0.237 32572 94.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.47 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 17 331 6438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236235
X-RAY DIFFRACTIONf_angle_d0.51518495
X-RAY DIFFRACTIONf_chiral_restr0.0416957
X-RAY DIFFRACTIONf_plane_restr0.00371109
X-RAY DIFFRACTIONf_dihedral_angle_d5.2653839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.34391310.24632008X-RAY DIFFRACTION86.35
2.41-2.480.33411400.23972139X-RAY DIFFRACTION93.02
2.48-2.550.29481400.23782134X-RAY DIFFRACTION93.97
2.55-2.630.3021440.23912197X-RAY DIFFRACTION95.4
2.63-2.730.28071440.24182211X-RAY DIFFRACTION95.07
2.73-2.830.34911450.24152223X-RAY DIFFRACTION95.91
2.83-2.960.34781450.25412219X-RAY DIFFRACTION97.04
2.96-3.120.29881490.23692282X-RAY DIFFRACTION97.67
3.12-3.320.27911460.24652230X-RAY DIFFRACTION96.47
3.32-3.570.26261450.2252215X-RAY DIFFRACTION96.29
3.57-3.930.26451470.21882241X-RAY DIFFRACTION96.21
3.93-4.50.20371470.19262241X-RAY DIFFRACTION95.87
4.5-5.670.23831430.1862199X-RAY DIFFRACTION93.38
5.67-48.210.28861340.19972033X-RAY DIFFRACTION84.55

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