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- PDB-23eg: Artificial Copper-binding dimeric protein 1 (Cu(I)DP1) -

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Basic information

Entry
Database: PDB / ID: 23eg
TitleArtificial Copper-binding dimeric protein 1 (Cu(I)DP1)
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsMETAL BINDING PROTEIN / Copper binding dimeric protein
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 (I) ION / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMethanothermobacter marburgensis str. Marburg (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsChoi, I. / Song, W.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Artificial Copper-binding dimeric protein 1 (Cu(I)DP1)
Authors: Choi, I. / Song, W.J.
History
DepositionFeb 3, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: 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
C: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2634
Polymers43,1362
Non-polymers1272
Water1,47782
1
A: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)43,2634
Polymers43,1362
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4040 Å2
ΔGint-10 kcal/mol
Surface area16530 Å2
MethodPISA
2
C: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

C: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2634
Polymers43,1362
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4230 Å2
ΔGint-15 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.629, 52.116, 79.322
Angle α, β, γ (deg.)90.000, 114.145, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-201-

CU1

21C-201-

CU1

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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: 21568.109 Da / Num. of mol.: 2 / Mutation: R79(BP5)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter marburgensis str. Marburg (archaea)
Gene: rmlC, MTH_1790 / Production host: Escherichia coli (E. coli)
References: UniProt: O27818, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl (pH 8.5) buffer with 0.2 M NaCl and 17 % (w/v) PEG 3350

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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: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.67→29.15 Å / Num. obs: 12305 / % possible obs: 98.6 % / Redundancy: 6.58 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.991 / Net I/σ(I): 9.48
Reflection shellResolution: 2.67→2.77 Å / Num. unique obs: 1865 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→29.15 Å / SU ML: 0.4665 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4745
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3221 616 5.01 %
Rwork0.2632 11689 -
obs0.2661 12305 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.02 Å2
Refinement stepCycle: LAST / Resolution: 2.67→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 2 82 3132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00173124
X-RAY DIFFRACTIONf_angle_d0.46484226
X-RAY DIFFRACTIONf_chiral_restr0.0454434
X-RAY DIFFRACTIONf_plane_restr0.0028560
X-RAY DIFFRACTIONf_dihedral_angle_d17.981160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.940.4321480.35142816X-RAY DIFFRACTION96.14
2.94-3.360.35611550.30372935X-RAY DIFFRACTION99.68
3.36-4.230.29551550.25052947X-RAY DIFFRACTION99.26
4.23-29.150.29761580.22942991X-RAY DIFFRACTION99.31

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