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- PDB-8yec: Crystal structure of L-ribulose 3-epimerase in complex with D-allulose -

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Basic information

Entry
Database: PDB / ID: 8yec
TitleCrystal structure of L-ribulose 3-epimerase in complex with D-allulose
ComponentsKetose 3-epimerase
KeywordsISOMERASE / D-allulose / ketose 3-epimerase / HYDROLASE
Function / homology
Function and homology information


Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / racemase and epimerase activity, acting on carbohydrates and derivatives / manganese ion binding / carbohydrate metabolic process
Similarity search - Function
: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
D-fructose / DI(HYDROXYETHYL)ETHER / D-psicose / Ketose 3-epimerase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWatanabe, M. / Nakamichi, Y. / Mine, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of L-ribulose 3-epimerase in complex with D-allulose
Authors: Watanabe, M. / Nakamichi, Y. / Mine, S.
History
DepositionFeb 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Ketose 3-epimerase
F: Ketose 3-epimerase
A: Ketose 3-epimerase
B: Ketose 3-epimerase
C: Ketose 3-epimerase
D: Ketose 3-epimerase
G: Ketose 3-epimerase
H: Ketose 3-epimerase
I: Ketose 3-epimerase
J: Ketose 3-epimerase
K: Ketose 3-epimerase
L: Ketose 3-epimerase
M: Ketose 3-epimerase
N: Ketose 3-epimerase
O: Ketose 3-epimerase
P: Ketose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,61773
Polymers517,17316
Non-polymers6,44457
Water10,485582
1
E: Ketose 3-epimerase
F: Ketose 3-epimerase
G: Ketose 3-epimerase
H: Ketose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,87818
Polymers129,2934
Non-polymers1,58414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-26 kcal/mol
Surface area38420 Å2
MethodPISA
2
A: Ketose 3-epimerase
B: Ketose 3-epimerase
C: Ketose 3-epimerase
D: Ketose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,98419
Polymers129,2934
Non-polymers1,69115
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-24 kcal/mol
Surface area38370 Å2
MethodPISA
3
I: Ketose 3-epimerase
J: Ketose 3-epimerase
M: Ketose 3-epimerase
N: Ketose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,87818
Polymers129,2934
Non-polymers1,58414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-22 kcal/mol
Surface area37970 Å2
MethodPISA
4
K: Ketose 3-epimerase
L: Ketose 3-epimerase
hetero molecules

O: Ketose 3-epimerase
P: Ketose 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,87818
Polymers129,2934
Non-polymers1,58414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area11340 Å2
ΔGint-26 kcal/mol
Surface area38580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.425, 135.131, 151.131
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 16 molecules EFABCDGHIJKLMNOP

#1: Protein
Ketose 3-epimerase / D-allulose 3-epimerase / D-AE / L-ribulose 3-epimerase


Mass: 32323.332 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: DAE / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1L7NQ96, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives

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Sugars , 2 types, 32 molecules

#2: Sugar
ChemComp-PSJ / D-psicose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-FUD / D-fructose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 607 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN
Nonpolymer detailsPSJ and FUD are in alternate conformations of each other.

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4000, 0.1M Sodium citrate/Citric acid pH5.5, 10% 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→47.2 Å / Num. obs: 625471 / % possible obs: 98.34 % / Redundancy: 3.5 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.06 / Rrim(I) all: 0.114 / Net I/σ(I): 8.25
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.6174 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 17606 / CC1/2: 0.853 / CC star: 0.959 / Rpim(I) all: 0.3809 / Rrim(I) all: 0.7271

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.325 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.681 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25452 8921 5 %RANDOM
Rwork0.20737 ---
obs0.20976 169505 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.01 Å2
2--0.08 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35808 0 415 582 36805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01236885
X-RAY DIFFRACTIONr_bond_other_d0.0010.01634207
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.63950000
X-RAY DIFFRACTIONr_angle_other_deg0.4361.56978710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15554662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.2155224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.854105855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.25664
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0243552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028368
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_it3.1324.65818696
X-RAY DIFFRACTIONr_mcbond_other3.1294.65918696
X-RAY DIFFRACTIONr_mcangle_it4.9198.3723342
X-RAY DIFFRACTIONr_mcangle_other4.9198.37123343
X-RAY DIFFRACTIONr_scbond_it3.625.02718189
X-RAY DIFFRACTIONr_scbond_other3.625.02718190
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9189.07526659
X-RAY DIFFRACTIONr_long_range_B_refined9.17156.45160513
X-RAY DIFFRACTIONr_long_range_B_other9.1756.44160410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.561 Å
RfactorNum. reflection% reflection
Rfree0.356 635 -
Rwork0.345 12063 -
obs--94.9 %

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