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- PDB-7dz5: Crystal structures of D-allulose 3-epimerase with D-sorbose from ... -

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Basic information

Entry
Database: PDB / ID: 7dz5
TitleCrystal structures of D-allulose 3-epimerase with D-sorbose from Sinorhizobium fredii
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / D-allulose / rare sugar / Sinorhizobium fredii / D-allulose 3-epimerase
Function / homologyracemase and epimerase activity, acting on carbohydrates and derivatives / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / manganese ion binding / alpha-D-Sorbopyranose / D-sorbose / D-tagatose 3-epimerase
Function and homology information
Biological speciesSinorhizobium fredii CCBAU 83666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhu, Z.L. / Miyakawa, T. / Tanokura, M. / Lu, F.P. / Qin, H.-M.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Substantial Improvement of an Epimerase for the Synthesis of D-Allulose by Biosensor-Based High-Throughput Microdroplet Screening
Authors: Li, C. / Gao, X. / Qi, H. / Zhang, W. / Li, L. / Wei, C. / Wei, M. / Sun, X. / Wang, S. / Wang, L. / Ji, Y. / Mao, S. / Zhu, Z. / Tanokura, M. / Lu, F. / Qin, H.M.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJan 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)125,49515
Polymers124,1374
Non-polymers1,35811
Water11,638646
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-8 kcal/mol
Surface area36810 Å2
Unit cell
Length a, b, c (Å)63.143, 87.934, 128.928
Angle α, β, γ (deg.)90.000, 99.579, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
D-tagatose 3-epimerase


Mass: 31034.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium fredii CCBAU 83666 (bacteria)
Gene: SF83666_b55120 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: A0A249Q1V1
#2: Sugar
ChemComp-SDD / D-sorbose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-HVC / alpha-D-Sorbopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG 3,350

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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 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→43.97 Å / Num. obs: 150697 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.047 / Rrim(I) all: 0.089 / Net I/σ(I): 0.089
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1.9 / CC1/2: 0.756 / Rpim(I) all: 0.346 / Rrim(I) all: 0.671 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZFS

5zfs


Resolution: 1.7→42.61 Å / SU ML: 0.1577 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.3469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.178 7655 5.08 %
Rwork0.153 143002 -
obs0.1543 150657 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8735 0 63 646 9444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00928986
X-RAY DIFFRACTIONf_angle_d1.059312190
X-RAY DIFFRACTIONf_chiral_restr0.05451332
X-RAY DIFFRACTIONf_plane_restr0.00691590
X-RAY DIFFRACTIONf_dihedral_angle_d9.09791233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.22692500.20624734X-RAY DIFFRACTION98.85
1.72-1.740.24262660.2044740X-RAY DIFFRACTION98.84
1.74-1.760.20992690.1964768X-RAY DIFFRACTION98.88
1.76-1.780.23542610.19154725X-RAY DIFFRACTION99.05
1.78-1.810.22162710.1894762X-RAY DIFFRACTION99.07
1.81-1.830.21392460.1694812X-RAY DIFFRACTION99.22
1.83-1.860.20652620.17414744X-RAY DIFFRACTION99.23
1.86-1.890.20342510.16844745X-RAY DIFFRACTION99.19
1.89-1.910.20792750.17184808X-RAY DIFFRACTION99.26
1.91-1.950.21062420.16644723X-RAY DIFFRACTION98.88
1.95-1.980.2062780.16284778X-RAY DIFFRACTION99.31
1.98-2.020.19752630.16414738X-RAY DIFFRACTION99.48
2.02-2.050.20032560.16474834X-RAY DIFFRACTION99.41
2.05-2.10.19632950.16074725X-RAY DIFFRACTION98.97
2.1-2.140.16822640.14944763X-RAY DIFFRACTION99.47
2.14-2.190.15842380.14754841X-RAY DIFFRACTION99.55
2.19-2.250.19322240.14784806X-RAY DIFFRACTION99.33
2.25-2.310.18372900.14694725X-RAY DIFFRACTION98.53
2.31-2.380.17362510.14434799X-RAY DIFFRACTION99.53
2.38-2.450.16442200.14384836X-RAY DIFFRACTION99.29
2.45-2.540.16422380.14864804X-RAY DIFFRACTION99.19
2.54-2.640.17442570.15124783X-RAY DIFFRACTION98.88
2.64-2.760.21082290.16034802X-RAY DIFFRACTION99.04
2.76-2.910.17622660.15954764X-RAY DIFFRACTION98.7
2.91-3.090.17862610.15774736X-RAY DIFFRACTION98.27
3.09-3.330.17722510.1584762X-RAY DIFFRACTION97.87
3.33-3.660.1582310.14664721X-RAY DIFFRACTION96.91
3.66-4.190.16022430.12614669X-RAY DIFFRACTION95.56
4.19-5.280.13282530.12044676X-RAY DIFFRACTION95.97
5.28-42.610.16912540.16424879X-RAY DIFFRACTION98.01

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