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- PDB-9uyw: Crystal structure of apo-form artificial metalloprotein incorpora... -

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Basic information

Entry
Database: PDB / ID: 9uyw
TitleCrystal structure of apo-form artificial metalloprotein incorporating a TP ligand
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsMETAL BINDING PROTEIN / noncanonical amino acids
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLee, Y.J. / Song, W.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2025-00523130 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2021-NR060082 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of apo-form artificial metalloprotein incorporating a TP ligand
Authors: Lee, Y.J. / Song, W.J.
History
DepositionMay 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dTDP-4-dehydrorhamnose 3,5-epimerase
B: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3195
Polymers44,2372
Non-polymers813
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-29 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.678, 72.428, 63.509
Angle α, β, γ (deg.)90.000, 113.844, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein dTDP-4-dehydrorhamnose 3,5-epimerase / Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D- ...Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D-xylo-4-hexulose 3 / dTDP-L-rhamnose synthase


Mass: 22118.723 Da / Num. of mol.: 2 / Mutation: R79 mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: rmlC, MTH_1790 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O27818, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1M NaH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.48→29.04 Å / Num. obs: 15252 / % possible obs: 97.2 % / Redundancy: 6.5 % / CC1/2: 0.998 / Net I/σ(I): 15.8
Reflection shellResolution: 2.48→2.57 Å / Num. unique obs: 1487 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→29.04 Å / SU ML: 0.3759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.88
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2668 755 5.01 %
Rwork0.2196 14327 -
obs0.222 15081 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.95 Å2
Refinement stepCycle: LAST / Resolution: 2.48→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 47 147 3237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193166
X-RAY DIFFRACTIONf_angle_d0.48994284
X-RAY DIFFRACTIONf_chiral_restr0.0451438
X-RAY DIFFRACTIONf_plane_restr0.0034567
X-RAY DIFFRACTIONf_dihedral_angle_d18.52621170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.670.3891500.27022859X-RAY DIFFRACTION99.37
2.67-2.940.30251510.25062861X-RAY DIFFRACTION99.41
2.94-3.370.28561500.22462846X-RAY DIFFRACTION98.62
3.37-4.240.23961500.1952848X-RAY DIFFRACTION97.69
4.24-29.040.22981540.20942913X-RAY DIFFRACTION98.74

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