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- PDB-9ja4: artificial dinuclear Zn-bound metalloprotein 2 (D2:Zn) -

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Basic information

Entry
Database: PDB / ID: 9ja4
Titleartificial dinuclear Zn-bound metalloprotein 2 (D2:Zn)
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
dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 24, 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
C: dTDP-4-dehydrorhamnose 3,5-epimerase
D: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,43912
Polymers85,9164
Non-polymers5238
Water36020
1
A: dTDP-4-dehydrorhamnose 3,5-epimerase
C: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2206
Polymers42,9582
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-134 kcal/mol
Surface area16620 Å2
MethodPISA
2
B: dTDP-4-dehydrorhamnose 3,5-epimerase
D: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2206
Polymers42,9582
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-138 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.494, 63.822, 73.524
Angle α, β, γ (deg.)89.95, 89.81, 66.28
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: 21478.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-d-hexulose 3, 5-epimerase (RmlC)
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Li2SO4, 0.1M MOPS, pH8.0 buffer, and 20 % PEG 4000

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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 EIGER2 S 9M / Detector: PIXEL / Date: Apr 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 23345 / % possible obs: 97.1 % / Redundancy: 3.45 % / CC1/2: 0.988 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.101 / Net I/σ(I): 6.59
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.7-2.860.28212060.8110.3991
2.86-3.050.18911860.920.2681
3.05-3.290.14810850.9560.211
3.29-3.60.0810080.9880.1141
3.6-4.020.0678520.990.0941
4.02-4.630.0637150.9830.091
4.63-5.630.0515770.9890.0731
5.63-7.820.0444370.9910.0621
7.82-300.0452340.9850.0631

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.24 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.869 / SU B: 27.86 / SU ML: 0.524 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29872 1166 5 %RANDOM
Rwork0.27535 ---
obs0.27655 22150 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.285 Å2
Baniso -1Baniso -2Baniso -3
1-10.48 Å22.16 Å20.42 Å2
2---3.89 Å20.25 Å2
3----3.19 Å2
Refinement stepCycle: 1 / Resolution: 2.7→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6008 0 8 20 6036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0126168
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165528
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.838362
X-RAY DIFFRACTIONr_angle_other_deg0.461.77712748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.879546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.193101010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021498
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_it2.433.5382924
X-RAY DIFFRACTIONr_mcbond_other2.4293.5382924
X-RAY DIFFRACTIONr_mcangle_it4.0286.3573648
X-RAY DIFFRACTIONr_mcangle_other4.0286.3583649
X-RAY DIFFRACTIONr_scbond_it2.6663.8873244
X-RAY DIFFRACTIONr_scbond_other2.6663.8873245
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5127.0074715
X-RAY DIFFRACTIONr_long_range_B_refined8.48143.224186
X-RAY DIFFRACTIONr_long_range_B_other8.4843.224182
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 84 -
Rwork0.403 1594 -
obs--93.43 %

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