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- PDB-7dz6: Crystal structures of D-allulose 3-epimerase with D-allulose from... -

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Basic information

Entry
Database: PDB / ID: 7dz6
TitleCrystal structures of D-allulose 3-epimerase with D-allulose 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 / D-psicose / D-tagatose 3-epimerase
Function and homology information
Biological speciesSinorhizobium fredii CCBAU 83666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhu, Z.L. / Miyakawa, T. / Tanokura, M. / Lu, F.P. / Qin, H.-M.
CitationJournal: 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.
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

Downloads & links

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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)125,80410
Polymers125,3464
Non-polymers4586
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-30 kcal/mol
Surface area36810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.558, 87.141, 128.881
Angle α, β, γ (deg.)90.000, 99.387, 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: 31336.531 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) / Variant (production host): Rosetta
References: UniProt: A0A249Q1V1, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-PSJ / D-psicose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
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: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.41 Å / Num. obs: 79743 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 34.62 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4533 / CC1/2: 0.752 / Rpim(I) all: 0.399

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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: 2.1→37.15 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2221 4078 5.12 %
Rwork0.1775 75619 -
obs0.1798 79697 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8737 0 15 163 8915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01348942
X-RAY DIFFRACTIONf_angle_d1.268912128
X-RAY DIFFRACTIONf_chiral_restr0.05781318
X-RAY DIFFRACTIONf_plane_restr0.00791590
X-RAY DIFFRACTIONf_dihedral_angle_d9.70631228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.32811220.28352593X-RAY DIFFRACTION99.89
2.12-2.150.29721540.25912585X-RAY DIFFRACTION100
2.15-2.180.30871220.25662608X-RAY DIFFRACTION100
2.18-2.210.30341410.2492577X-RAY DIFFRACTION100
2.21-2.240.31241300.24482657X-RAY DIFFRACTION99.93
2.24-2.270.29741370.23822550X-RAY DIFFRACTION100
2.27-2.30.26531410.23372614X-RAY DIFFRACTION99.93
2.3-2.340.30521660.23312570X-RAY DIFFRACTION99.93
2.34-2.380.29071390.22772578X-RAY DIFFRACTION99.96
2.38-2.420.25721550.2222629X-RAY DIFFRACTION99.89
2.42-2.460.28981270.21562572X-RAY DIFFRACTION100
2.46-2.510.3091220.21672631X-RAY DIFFRACTION100
2.51-2.560.25261490.21072576X-RAY DIFFRACTION99.96
2.56-2.620.26781310.20252667X-RAY DIFFRACTION99.93
2.62-2.680.22441240.20572572X-RAY DIFFRACTION99.93
2.68-2.740.28041270.21062635X-RAY DIFFRACTION100
2.74-2.820.24781450.21462617X-RAY DIFFRACTION100
2.82-2.90.28031300.20752587X-RAY DIFFRACTION100
2.9-2.990.23791450.20572634X-RAY DIFFRACTION99.89
2.99-3.10.24451540.2012560X-RAY DIFFRACTION99.93
3.1-3.230.26771320.20362619X-RAY DIFFRACTION99.93
3.23-3.370.2241330.19472629X-RAY DIFFRACTION100
3.37-3.550.23311290.17162618X-RAY DIFFRACTION99.93
3.55-3.770.21041280.15192612X-RAY DIFFRACTION100
3.77-4.060.23051700.13762605X-RAY DIFFRACTION99.93
4.06-4.470.14131590.1252627X-RAY DIFFRACTION99.68
4.47-5.120.15591400.1222613X-RAY DIFFRACTION99.85
5.12-6.440.18231580.14882614X-RAY DIFFRACTION99.46
6.44-37.150.16991680.13992670X-RAY DIFFRACTION99.68

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