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- PDB-9j9v: artificial dinuclear Fe-bound metalloprotein 2 (D2:Fe) -

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Basic information

Entry
Database: PDB / ID: 9j9v
Titleartificial dinuclear Fe-bound metalloprotein 2 (D2:Fe)
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: 2.04 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
C: dTDP-4-dehydrorhamnose 3,5-epimerase
D: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,36312
Polymers85,9164
Non-polymers4478
Water6,557364
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)43,1816
Polymers42,9582
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3670 Å2
ΔGint-55 kcal/mol
Surface area16270 Å2
MethodPISA
2
C: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)43,1816
Polymers42,9582
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3650 Å2
ΔGint-55 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.012, 63.999, 73.218
Angle α, β, γ (deg.)90.01, 90.04, 113.85
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)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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Li2SO4, 0.1M HEPES 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: May 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. obs: 52907 / % possible obs: 96 % / Redundancy: 3.52 % / CC1/2: 0.996 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.061 / Net I/σ(I): 7.67
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.04-2.170.21831360.8820.3081
2.17-2.310.17430200.9320.2461
2.31-2.50.12226490.9680.1721
2.5-2.730.123870.9790.1411
2.73-3.050.06320930.990.0891
3.05-3.520.04318440.9940.0611
3.52-4.30.03614500.9940.0521
4.3-6.010.03510510.9940.051
6.01-300.0345410.9930.0481

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→29.27 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.617 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26688 2646 5 %RANDOM
Rwork0.23946 ---
obs0.24085 50258 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.126 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.42 Å2-0.12 Å2
2---1.6 Å2-0.15 Å2
3---2.91 Å2
Refinement stepCycle: 1 / Resolution: 2.04→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5996 0 8 364 6368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126156
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165508
X-RAY DIFFRACTIONr_angle_refined_deg1.561.8298348
X-RAY DIFFRACTIONr_angle_other_deg0.5821.77512704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9075728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.919544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.672101004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021488
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_it3.082.8022924
X-RAY DIFFRACTIONr_mcbond_other3.082.8022924
X-RAY DIFFRACTIONr_mcangle_it4.1285.0113648
X-RAY DIFFRACTIONr_mcangle_other4.1275.013649
X-RAY DIFFRACTIONr_scbond_it4.5433.3793232
X-RAY DIFFRACTIONr_scbond_other4.5423.3783233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7525.9714701
X-RAY DIFFRACTIONr_long_range_B_refined8.61237.8825213
X-RAY DIFFRACTIONr_long_range_B_other8.59137.5424996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.042→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 183 -
Rwork0.262 3467 -
obs--90.12 %

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