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- PDB-9kcs: Crystal structure of Tagatose 4-epimerase with one glycerol from ... -

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Basic information

Entry
Database: PDB / ID: 9kcs
TitleCrystal structure of Tagatose 4-epimerase with one glycerol from Thermoprotei archaeon
ComponentsISOMERASE
KeywordsISOMERASE
Function / homologyChem-1PG / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesThermoprotei archaeon (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsChen, J. / Luo, G. / Huang, Z. / Ni, D. / Zhu, Y. / Xu, W. / Zhang, W. / Mu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2022YFC2104900 China
CitationJournal: To Be Published
Title: Crystal structure of Tagatose 4-epimerase with one glycerol from Thermoprotei archaeon
Authors: Chen, J. / Luo, G. / Huang, Z. / Ni, D. / Zhu, Y. / Xu, W. / Zhang, W. / Mu, W.
History
DepositionNov 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,32316
Polymers57,0871
Non-polymers1,23615
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.420, 76.230, 90.930
Angle α, β, γ (deg.)90.00, 100.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-888-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ISOMERASE


Mass: 57087.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AUTHORS STATE THAT THE NCBI ACCESSION NUMBER IS RLE72111.1 FOR THE PROTEIN.
Source: (gene. exp.) Thermoprotei archaeon (archaea) / Gene: DRJ37_03570 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A662GG58

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Non-polymers , 6 types, 235 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5 42% v/v Polyethylene glycol 200 5 mM Nickel sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jun 5, 2024 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.13→45.64 Å / Num. obs: 31435 / % possible obs: 95.9 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 11.3
Reflection shellResolution: 2.13→2.19 Å / Num. unique obs: 2570 / CC1/2: 0.729

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→45.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.367 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21717 1519 4.8 %RANDOM
Rwork0.17553 ---
obs0.17752 29911 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.468 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å2-1.53 Å2
2--0.28 Å20 Å2
3----1.08 Å2
Refinement stepCycle: 1 / Resolution: 2.13→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 78 220 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194114
X-RAY DIFFRACTIONr_bond_other_d0.0010.023997
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9935506
X-RAY DIFFRACTIONr_angle_other_deg0.76739220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99923.102187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59915740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9021534
X-RAY DIFFRACTIONr_chiral_restr0.0760.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024504
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
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_it1.9083.1471969
X-RAY DIFFRACTIONr_mcbond_other1.9033.1451968
X-RAY DIFFRACTIONr_mcangle_it2.9344.7092461
X-RAY DIFFRACTIONr_mcangle_other2.9334.712462
X-RAY DIFFRACTIONr_scbond_it2.5653.4842145
X-RAY DIFFRACTIONr_scbond_other2.5653.4842145
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1425.0833043
X-RAY DIFFRACTIONr_long_range_B_refined5.76637.6314915
X-RAY DIFFRACTIONr_long_range_B_other5.69837.444846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.132→2.187 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 128 -
Rwork0.257 2181 -
obs--95.69 %

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