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- PDB-9kyn: artificial dinuclear Cu-bound metalloprotein 3 (D3:Cu) -

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Basic information

Entry
Database: PDB / ID: 9kyn
Titleartificial dinuclear Cu-bound metalloprotein 3 (D3:Cu)
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsISOMERASE / Thermophilic isomerase
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJeong, W.J. / Song, W.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other private2019R1C1C1003863 Korea, Republic Of
CitationJournal: To Be Published
Title: Metal-Installer: A protein designer tool to create metal-binding sites
Authors: Jeong, W.J. / Song, W.J.
History
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)42,9734
Polymers42,8462
Non-polymers1272
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.900, 52.498, 60.802
Angle α, β, γ (deg.)110.83, 107.43, 95.81
Int Tables number1
Space group name H-MP1

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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: 21422.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rmlC, MTH_1790 / Production host: Escherichia coli (E. coli)
References: UniProt: O27818, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Li2SO4, 20 % PEG 4000, pH 8.0 0.1M MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00311 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00311 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 20609 / % possible obs: 96.6 % / Redundancy: 3.2 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.071 / Rrim(I) all: 0.131 / Χ2: 3.015 / Net I/σ(I): 9.6 / Num. measured all: 65431
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.342.60.3410570.8930.9710.2330.4140.67495.3
2.34-2.382.70.35110060.8780.9670.2370.4250.67795.6
2.38-2.432.90.32810180.8920.9710.220.3960.68996.5
2.43-2.482.90.3310670.8960.9720.220.3980.69696.8
2.48-2.533.10.3110050.9060.9750.2030.3720.82696.7
2.53-2.593.10.29310280.9070.9750.1910.3510.93297.1
2.59-2.653.20.26610560.9240.980.1720.3181.13296.9
2.65-2.733.30.25410020.9320.9820.1620.3021.13697.1
2.73-2.813.30.23510440.9470.9860.150.281.19396.6
2.81-2.93.30.18910280.9620.990.1190.2241.58696.4
2.9-33.20.16410220.9710.9930.1070.1971.51196.4
3-3.1230.13810020.9680.9920.0950.1691.90795.1
3.12-3.263.20.12510490.9760.9940.080.1492.40196.9
3.26-3.433.60.10910480.980.9950.0680.1292.67698.3
3.43-3.653.50.11510370.9810.9950.070.1353.55798.1
3.65-3.933.50.08810350.9880.9970.0560.1054.04697.5
3.93-4.333.40.07910560.9840.9960.050.0944.56198.1
4.33-4.953.20.08110110.9810.9950.0520.0966.48994
4.95-6.2330.0769900.9710.9930.0520.09310.03994.6
6.23-103.40.0810480.9790.9950.0520.09611.32597.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1.5286refinement
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.93 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 940 4.57 %
Rwork0.1991 --
obs0.2011 20573 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 2 15 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083104
X-RAY DIFFRACTIONf_angle_d0.8664206
X-RAY DIFFRACTIONf_dihedral_angle_d19.9881152
X-RAY DIFFRACTIONf_chiral_restr0.057430
X-RAY DIFFRACTIONf_plane_restr0.008562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.30091320.23362737X-RAY DIFFRACTION94
2.42-2.570.29571510.23832789X-RAY DIFFRACTION97
2.57-2.770.29381300.2362856X-RAY DIFFRACTION97
2.77-3.050.27991480.22712780X-RAY DIFFRACTION96
3.05-3.490.23151210.20162828X-RAY DIFFRACTION97
3.49-4.40.24091280.18082856X-RAY DIFFRACTION98
4.4-100.19351300.17712787X-RAY DIFFRACTION95

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