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- PDB-9j9r: artificial mononuclear Zn-bound metalloprotein 6 (M6:Zn) -

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Basic information

Entry
Database: PDB / ID: 9j9r
Titleartificial mononuclear Zn-bound metalloprotein 6 (M6: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: 2.6 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
Revision 1.1Jul 23, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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)86,3908
Polymers86,1284
Non-polymers2624
Water724
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)43,1954
Polymers43,0642
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3360 Å2
ΔGint-83 kcal/mol
Surface area16340 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)43,1954
Polymers43,0642
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_544x,y-1,z-11
Buried area3310 Å2
ΔGint-82 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.456, 63.515, 71.491
Angle α, β, γ (deg.)90.12, 89.76, 65.59
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.: 4
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 51.16 %
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: 0.97934 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: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.57→30 Å / Num. obs: 24882 / % possible obs: 94.8 % / Redundancy: 3.1 % / CC1/2: 0.972 / CC star: 0.993 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.082 / Rrim(I) all: 0.149 / Χ2: 2.773 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.20.44712730.8510.9590.2930.5370.72893.1
2.64-2.693.20.4111590.8430.9570.2620.4890.68193.2
2.69-2.743.10.3612420.860.9620.2420.4360.73993.9
2.74-2.83.10.32912130.8740.9660.2220.3990.81392
2.8-2.863.10.31912320.8910.9710.2180.3890.8894.7
2.86-2.932.90.26612340.8970.9720.1890.3280.88491.7
2.93-33.10.22611880.9350.9830.1510.2730.96890.8
3-3.083.20.21412250.9260.980.1390.2571.11693
3.08-3.173.30.19712220.9330.9830.1280.2361.43693.4
3.17-3.283.20.16912480.9530.9880.1110.2031.58494.2
3.28-3.393.20.14112440.960.990.0930.1692.12796
3.39-3.533.20.13212530.9550.9880.0860.1582.28295.1
3.53-3.693.20.11512570.9770.9940.0750.1382.06596.5
3.69-3.883.10.1112550.9710.9920.0740.1333.16896.3
3.88-4.1230.112950.9680.9920.0680.1224.25797.9
4.12-4.442.90.08912650.9780.9940.0630.114.66196.9
4.44-4.8930.07713030.9790.9950.0530.0944.3997.6
4.89-5.593.10.07912590.9750.9940.0540.0964.08597.5
5.59-7.033.10.0712730.9890.9970.0460.0853.2596.8
7.03-303.30.07912420.9750.9940.0530.09514.47294.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.93 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.867 / SU B: 16.099 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27937 1160 4.7 %RANDOM
Rwork0.2232 ---
obs0.22583 23324 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.688 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å21.57 Å2-1.62 Å2
2---2.83 Å21.05 Å2
3---3.44 Å2
Refinement stepCycle: 1 / Resolution: 2.6→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6088 0 4 4 6096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126248
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165656
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.8358464
X-RAY DIFFRACTIONr_angle_other_deg0.5411.78213028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2065728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.492556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.054101044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021556
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_it2.3532.8752924
X-RAY DIFFRACTIONr_mcbond_other2.3532.8752924
X-RAY DIFFRACTIONr_mcangle_it3.765.163648
X-RAY DIFFRACTIONr_mcangle_other3.7595.163649
X-RAY DIFFRACTIONr_scbond_it2.7683.2313324
X-RAY DIFFRACTIONr_scbond_other2.7683.2313325
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4915.7784817
X-RAY DIFFRACTIONr_long_range_B_refined7.37139.3825064
X-RAY DIFFRACTIONr_long_range_B_other7.37139.3825065
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 116 -
Rwork0.277 1655 -
obs--92.97 %

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