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- PDB-7e9w: The Crystal Structure of D-psicose-3-epimerase from Biortus. -

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Basic information

Entry
Database: PDB / ID: 7e9w
TitleThe Crystal Structure of D-psicose-3-epimerase from Biortus.
ComponentsD-psicose 3-epimerase
KeywordsISOMERASE / ion binding / cation binding / metal ion binding
Function / homology
Function and homology information


D-psicose 3-epimerase / racemase and epimerase activity, acting on carbohydrates and derivatives / cobalt ion binding / manganese ion binding
Similarity search - Function
: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / D-psicose 3-epimerase
Similarity search - Component
Biological speciesRuminiclostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, F. / Xu, C. / Qi, J. / Zhang, M. / Tian, F. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
The Natural Science Foundation of Jiangsu ProvinceBK20170222 China
CitationJournal: To Be Published
Title: The Crystal Structure of D-psicose-3-epimerase from Biortus.
Authors: Wang, F. / Xu, C. / Qi, J. / Zhang, M. / Tian, F. / Wang, M.
History
DepositionMar 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,09420
Polymers143,7694
Non-polymers1,32516
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-33 kcal/mol
Surface area41540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.134, 116.083, 91.817
Angle α, β, γ (deg.)90.000, 105.083, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-psicose 3-epimerase / DPEase


Mass: 35942.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10) (bacteria)
Strain: ATCC 35319 / DSM 5812 / JCM 6584 / H10 / Gene: Ccel_0941 / Production host: Escherichia coli (E. coli) / References: UniProt: B8I944, D-psicose 3-epimerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02M MgCl2, 0.1M HEPES pH7.5, 22% Polyacrylic acid sodium salt 5,100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.5215 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5215 Å / Relative weight: 1
ReflectionResolution: 2.1→48.607 Å / Num. obs: 91449 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 4468 / CC1/2: 0.829

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vni

3vni


Resolution: 2.1→48.607 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.174 / SU B: 4.045 / SU ML: 0.104 / Average fsc free: 0.9328 / Average fsc work: 0.9416 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2058 4559 4.986 %
Rwork0.1737 86880 -
all0.175 --
obs-91439 97.957 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.358 Å20 Å21.476 Å2
2---0.369 Å2-0 Å2
3----0.685 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9212 0 76 574 9862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139520
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178649
X-RAY DIFFRACTIONr_angle_refined_deg1.221.63412848
X-RAY DIFFRACTIONr_angle_other_deg1.1931.5820049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54451160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17222.896518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96151586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0041552
X-RAY DIFFRACTIONr_chiral_restr0.0530.21182
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022038
X-RAY DIFFRACTIONr_nbd_refined0.1870.21981
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.28452
X-RAY DIFFRACTIONr_nbtor_refined0.160.24604
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2632
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1180.211
X-RAY DIFFRACTIONr_nbd_other0.1760.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0840.212
X-RAY DIFFRACTIONr_mcbond_it1.4413.5214640
X-RAY DIFFRACTIONr_mcbond_other1.443.524639
X-RAY DIFFRACTIONr_mcangle_it2.3275.2735794
X-RAY DIFFRACTIONr_mcangle_other2.3265.2745795
X-RAY DIFFRACTIONr_scbond_it1.8733.814880
X-RAY DIFFRACTIONr_scbond_other1.8723.8114881
X-RAY DIFFRACTIONr_scangle_it2.9125.6097052
X-RAY DIFFRACTIONr_scangle_other2.9125.6097053
X-RAY DIFFRACTIONr_lrange_it4.5341.52811058
X-RAY DIFFRACTIONr_lrange_other4.43441.33810925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.2693230.2356291X-RAY DIFFRACTION95.9524
2.155-2.2140.2673310.2256092X-RAY DIFFRACTION96.3257
2.214-2.2780.2392980.2126071X-RAY DIFFRACTION97.0145
2.278-2.3480.2633060.2095831X-RAY DIFFRACTION97.5056
2.348-2.4250.2343330.2035698X-RAY DIFFRACTION97.5101
2.425-2.510.2282760.1975513X-RAY DIFFRACTION97.8367
2.51-2.6040.2322580.195353X-RAY DIFFRACTION98.0944
2.604-2.7110.2132560.1885171X-RAY DIFFRACTION98.0665
2.711-2.8310.2042370.1844987X-RAY DIFFRACTION98.3804
2.831-2.9690.2162410.1844735X-RAY DIFFRACTION98.5737
2.969-3.1290.2342730.1934456X-RAY DIFFRACTION98.3978
3.129-3.3190.2242280.1874305X-RAY DIFFRACTION98.6722
3.319-3.5480.2192430.1793973X-RAY DIFFRACTION98.7585
3.548-3.8320.1881780.1613803X-RAY DIFFRACTION99.1285
3.832-4.1970.1731860.1453453X-RAY DIFFRACTION98.9396
4.197-4.6910.1571510.1263157X-RAY DIFFRACTION99.1607
4.691-5.4140.161560.1382776X-RAY DIFFRACTION99.2217
5.414-6.6240.211330.1732357X-RAY DIFFRACTION99.3615
6.624-9.3420.145910.1291847X-RAY DIFFRACTION99.4867
9.342-48.6070.152610.1451011X-RAY DIFFRACTION97.1895

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