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Basic information

Entry
Database: PDB / ID: 9var
TitleCrystal structure of Cu-bound 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
COPPER (II) ION / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.862 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 Cu-bound artificial metalloprotein incorporating a TP ligand
Authors: Lee, Y.J. / Song, W.J.
History
DepositionJun 4, 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
C: dTDP-4-dehydrorhamnose 3,5-epimerase
D: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,87111
Polymers88,4754
Non-polymers3967
Water3,009167
1
A: dTDP-4-dehydrorhamnose 3,5-epimerase
B: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3885
Polymers44,2372
Non-polymers1503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-32 kcal/mol
Surface area16660 Å2
MethodPISA
2
C: dTDP-4-dehydrorhamnose 3,5-epimerase
D: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4846
Polymers44,2372
Non-polymers2464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-41 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.582, 72.741, 63.520
Angle α, β, γ (deg.)90.047, 113.492, 89.894
Int Tables number1
Space group name H-MP1
Space group name HallP1

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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.: 4 / 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1M CHES, 0.2M NaCl, 1.1M ammonium sulfate

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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: 2.862→29.13 Å / Num. obs: 18157 / % possible obs: 91.9 % / Redundancy: 3.33 % / CC1/2: 0.99 / Net I/σ(I): 10.75
Reflection shellResolution: 2.862→2.964 Å / Num. unique obs: 1763 / CC1/2: 0.956 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.862→29.13 Å / SU ML: 0.3453 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.1896
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 908 5.01 %
Rwork0.2248 17231 -
obs0.2272 18139 92.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.22 Å2
Refinement stepCycle: LAST / Resolution: 2.862→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 99 167 6352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196336
X-RAY DIFFRACTIONf_angle_d0.45368574
X-RAY DIFFRACTIONf_chiral_restr0.0438876
X-RAY DIFFRACTIONf_plane_restr0.0031134
X-RAY DIFFRACTIONf_dihedral_angle_d18.23512340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.862-3.040.2951540.26482932X-RAY DIFFRACTION94.46
3.04-3.280.32581570.2522980X-RAY DIFFRACTION97.39
3.28-3.60.31661500.23722843X-RAY DIFFRACTION91.75
3.6-4.120.26661360.21542583X-RAY DIFFRACTION84.81
4.12-5.190.24691520.18432892X-RAY DIFFRACTION92.05
5.19-29.130.24421590.23893001X-RAY DIFFRACTION97.23

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