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- PDB-8xiv: Production of D-psicose -

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Basic information

Entry
Database: PDB / ID: 8xiv
TitleProduction of D-psicose
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / D-tagatose 3-epimerase
Function / homology: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / : / D-fructose / D-tagatose 3-epimerase
Function and homology information
Biological speciesKroppenstedtia eburnea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGuo, D.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: Production of D-psicose
Authors: Guo, D.
History
DepositionDec 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-tagatose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5425
Polymers33,1191
Non-polymers4234
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.056, 121.056, 47.433
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

#1: Protein D-tagatose 3-epimerase


Mass: 33118.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kroppenstedtia eburnea (bacteria) / Gene: SAMN05421790_10663 / Production host: Kroppenstedtia eburnea (bacteria) / References: UniProt: A0A1N7MFN7
#2: Sugar ChemComp-FUD / D-fructose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop
Details: 2% v/v 1,4-dioxane 0.1 M Tris pH 8.0 15% w/v Polyethlene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→24.98 Å / Num. obs: 47060 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 0.998
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2252 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VNK

3vnk


Resolution: 1.6→24.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.421 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19571 2409 5.1 %RANDOM
Rwork0.16209 ---
obs0.16375 44595 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.492 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.6→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 25 286 2645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132489
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162408
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.6473376
X-RAY DIFFRACTIONr_angle_other_deg1.4191.5915563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38422.391138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55415458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7721517
X-RAY DIFFRACTIONr_chiral_restr0.0760.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.061.1991185
X-RAY DIFFRACTIONr_mcbond_other1.0471.1971184
X-RAY DIFFRACTIONr_mcangle_it1.6411.7941486
X-RAY DIFFRACTIONr_mcangle_other1.6421.7971487
X-RAY DIFFRACTIONr_scbond_it2.0051.4631303
X-RAY DIFFRACTIONr_scbond_other2.0041.4651304
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.172.0961878
X-RAY DIFFRACTIONr_long_range_B_refined4.5215.5282970
X-RAY DIFFRACTIONr_long_range_B_other4.35715.0362897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å
RfactorNum. reflection% reflection
Rfree0.282 196 -
Rwork0.245 3149 -
obs--97.58 %

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