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- PDB-8xj1: Structure of Apo-KeDt3e -

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Basic information

Entry
Database: PDB / ID: 8xj1
TitleStructure of Apo-KeDt3e
ComponentsD-tagatose 3-epimerase
KeywordsISOMERASE / D-tagatose 3-epimerase
Function / homology: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / D-tagatose 3-epimerase
Function and homology information
Biological speciesKroppenstedtia eburnea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsGuo, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Production of D-psicose
Authors: Guo, D.Y.
History
DepositionDec 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-tagatose 3-epimerase


Theoretical massNumber of molelcules
Total (without water)33,0321
Polymers33,0321
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12590 Å2
Unit cell
Length a, b, c (Å)119.310, 119.310, 47.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein D-tagatose 3-epimerase


Mass: 33031.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kroppenstedtia eburnea (bacteria) / Gene: SAMN05421790_10663 / Production host: Kroppenstedtia eburnea (bacteria) / References: UniProt: A0A1N7MFN7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 229 K / Method: vapor diffusion, hanging drop
Details: 2% v/v 1,4-dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethlene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.16→47.87 Å / Num. obs: 19137 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6
Reflection shellResolution: 2.16→2.23 Å / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1606

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→44.47 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.225 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25477 977 5.1 %RANDOM
Rwork0.20299 ---
obs0.20558 18116 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.248 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.16→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 0 72 2391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132369
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162256
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.6413201
X-RAY DIFFRACTIONr_angle_other_deg1.1611.5865193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30522.652132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78815423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6791515
X-RAY DIFFRACTIONr_chiral_restr0.0520.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
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_it0.6342.4531151
X-RAY DIFFRACTIONr_mcbond_other0.6342.4521149
X-RAY DIFFRACTIONr_mcangle_it1.0453.6761436
X-RAY DIFFRACTIONr_mcangle_other1.0453.6761436
X-RAY DIFFRACTIONr_scbond_it0.8052.5711217
X-RAY DIFFRACTIONr_scbond_other0.8052.5721218
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3613.8121765
X-RAY DIFFRACTIONr_long_range_B_refined2.59128.3712628
X-RAY DIFFRACTIONr_long_range_B_other2.47528.2322615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 71 -
Rwork0.263 1306 -
obs--98.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0685-1.10771.94891.1842-1.01631.4631-0.2844-0.11270.20310.25710.0989-0.1161-0.02540.06220.18550.22760.13770.01640.11150.020.025239.799911.732715.6196
23.08421.0883-0.88840.8425-0.4390.8869-0.0562-0.23390.06140.07880.02260.0234-0.05190.05470.03360.06010.0224-0.02620.04330.00310.067149.12969.641613.9035
30.77440.0454-0.1192.2235-0.63020.71740.04550.11610.06550.1108-0.0483-0.1243-0.04710.05960.00280.04180.00650.00490.0476-0.00230.059351.537819.7768-0.2671
41.5297-0.2993-0.01720.6706-0.17220.06560.02050.2052-0.0313-0.0058-0.0320.00590.006-0.00950.01150.05140.0221-0.0060.0955-0.0310.01737.613816.9105-5.3137
51.3725-0.69170.73680.5733-0.56190.56830.10950.0289-0.3302-0.0051-0.00980.09370.04640.007-0.09970.10760.0004-0.02120.0379-0.05360.162927.51094.1428-0.5328
61.4524-2.1344-0.61744.468-1.60825.04470.005-0.03850.25970.0733-0.0312-0.4285-0.17420.15920.02620.07470.0425-0.04470.0436-0.04650.12231.970225.445713.8285
74.91764.19535.65135.85046.12658.4474-0.1706-0.20710.04040.40150.03030.23040.2563-0.25920.14030.15550.03670.03760.05260.03040.034426.79968.22415.8934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 61
2X-RAY DIFFRACTION2A62 - 92
3X-RAY DIFFRACTION3A93 - 133
4X-RAY DIFFRACTION4A134 - 258
5X-RAY DIFFRACTION5A259 - 277
6X-RAY DIFFRACTION6A278 - 302
7X-RAY DIFFRACTION7A303 - 322

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