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- PDB-7ero: Crystal structure of D-allulose 3-epimerase with D-allulose from ... -

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Basic information

Entry
Database: PDB / ID: 7ero
TitleCrystal structure of D-allulose 3-epimerase with D-allulose from Agrobacterium sp. SUL3
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / D-allulose / rare sugar / Agrobacterium sp. SUL3 / D-allulose 3-epimerase
Function / homologyXylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / D-psicose / D-tagatose 3-epimerase
Function and homology information
Biological speciesAgrobacterium sp. SUL3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsZhu, Z.L. / Miyakawa, T. / Tanokura, M. / Lu, F.P. / Qin, H.-M.
CitationJournal: Adv Sci / Year: 2024
Title: Growth-Coupled Evolutionary Pressure Improving Epimerases for D-Allulose Biosynthesis Using a Biosensor-Assisted In Vivo Selection Platform
Authors: Li, C. / Gao, H. / Li, H. / Wang, T. / Lu, F.P. / Qin, H.-M.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,15912
Polymers122,3424
Non-polymers8188
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-18 kcal/mol
Surface area37030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.173, 97.517, 159.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
D-tagatose 3-epimerase


Mass: 30585.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium sp. SUL3 (bacteria) / Gene: AKG12_23230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: A0A0L6K0Q2, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Sugar
ChemComp-PSJ / D-psicose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride, 0.1M Tris pH=8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.12→48.76 Å / Num. obs: 59560 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.08 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.096 / Rrim(I) all: 0.25 / Net I/σ(I): 9
Reflection shellResolution: 2.12→2.18 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4561 / CC1/2: 0.693 / Rpim(I) all: 0.559

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DZ2

7dz2


Resolution: 2.12→48.76 Å / SU ML: 0.2447 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 3072 5.17 %
Rwork0.18 56395 -
obs0.1825 59467 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.53 Å2
Refinement stepCycle: LAST / Resolution: 2.12→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8624 0 4 367 8995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00758816
X-RAY DIFFRACTIONf_angle_d0.877111966
X-RAY DIFFRACTIONf_chiral_restr0.05011313
X-RAY DIFFRACTIONf_plane_restr0.00521573
X-RAY DIFFRACTIONf_dihedral_angle_d8.45561220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.150.30621500.24512484X-RAY DIFFRACTION99.77
2.15-2.190.3161370.23912547X-RAY DIFFRACTION99.96
2.19-2.230.27941300.23292531X-RAY DIFFRACTION99.92
2.23-2.270.29521470.24192526X-RAY DIFFRACTION100
2.27-2.310.28891550.2352516X-RAY DIFFRACTION99.93
2.31-2.360.29571380.23412530X-RAY DIFFRACTION100
2.36-2.410.32241240.22182530X-RAY DIFFRACTION99.96
2.41-2.460.24521300.21222558X-RAY DIFFRACTION99.78
2.46-2.530.2841360.21342528X-RAY DIFFRACTION99.85
2.53-2.590.23831390.21062523X-RAY DIFFRACTION99.96
2.59-2.670.30921240.20972570X-RAY DIFFRACTION100
2.67-2.760.26931480.21992562X-RAY DIFFRACTION100
2.76-2.860.2831280.20462546X-RAY DIFFRACTION99.96
2.86-2.970.25431460.20252558X-RAY DIFFRACTION99.93
2.97-3.110.26411310.20262559X-RAY DIFFRACTION99.96
3.11-3.270.27481450.20052574X-RAY DIFFRACTION100
3.27-3.470.25561190.17882602X-RAY DIFFRACTION99.89
3.47-3.740.19881570.15612554X-RAY DIFFRACTION99.96
3.74-4.120.15471650.13992563X-RAY DIFFRACTION100
4.12-4.710.17261340.12732632X-RAY DIFFRACTION100
4.71-5.940.18511370.14422635X-RAY DIFFRACTION100
5.94-48.760.17011520.1542767X-RAY DIFFRACTION99.79

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