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- PDB-9j9q: artificial mononuclear Cu-bound metalloprotein 6 (M6:Cu) -

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Basic information

Entry
Database: PDB / ID: 9j9q
Titleartificial mononuclear Cu-bound metalloprotein 6 (M6: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 speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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
DepositionAug 23, 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)43,1914
Polymers43,0642
Non-polymers1272
Water2,126118
1
A: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)43,1914
Polymers43,0642
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area3430 Å2
ΔGint-28 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.467, 52.250, 55.880
Angle α, β, γ (deg.)100.87, 100.39, 112.11
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: 21531.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
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.: 118 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
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: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.49→27.36 Å / Num. obs: 14194 / % possible obs: 97 % / Redundancy: 3.49 % / CC1/2: 0.997 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.045 / Net I/σ(I): 10.72
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.49-2.640.0588210.9910.0821
2.64-2.820.0477190.9910.0671
2.82-3.050.0396830.9920.0551
3.05-3.340.0345870.9940.0481
3.34-3.720.0345030.9930.0481
3.72-4.280.0274510.9970.0391
4.28-5.220.0273680.9950.0391
5.22-7.250.0352420.9930.0491
7.25-27.360.031460.9960.0431

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→27.36 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.854 / SU B: 12.816 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 1.138 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29039 710 5 %RANDOM
Rwork0.23171 ---
obs0.23469 13484 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.084 Å2
Baniso -1Baniso -2Baniso -3
1-4.41 Å2-0.06 Å2-1.63 Å2
2---1.89 Å2-1.15 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.49→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 2 118 3156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123116
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162822
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.8334222
X-RAY DIFFRACTIONr_angle_other_deg0.491.7826496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7855364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.637528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08510518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
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_it1.9882.5151462
X-RAY DIFFRACTIONr_mcbond_other1.9882.5151462
X-RAY DIFFRACTIONr_mcangle_it3.2624.5091824
X-RAY DIFFRACTIONr_mcangle_other3.2624.5081825
X-RAY DIFFRACTIONr_scbond_it2.5672.9231654
X-RAY DIFFRACTIONr_scbond_other2.5662.9231655
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3285.1972399
X-RAY DIFFRACTIONr_long_range_B_refined7.04433.1712579
X-RAY DIFFRACTIONr_long_range_B_other7.0333.1912548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.494→2.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 51 -
Rwork0.309 969 -
obs--94.71 %

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