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- PDB-9quo: Co(II)-bound de novo protein scaffold TFD-EH T87E -

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Basic information

Entry
Database: PDB / ID: 9quo
TitleCo(II)-bound de novo protein scaffold TFD-EH T87E
ComponentsTFD-EH T87E
KeywordsDE NOVO PROTEIN / TIM barrel / Enzyme Engineering / Metal Coordination / Conformational Dynamics
Function / homology: / IMIDAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWagner Egea, P. / Delhommel, F. / Mustafa, G. / Leiss-Maier, F. / Klimper, L. / Badmann, T. / Heider, A. / Wille, I.C. / Groll, M. / Sattler, M. / Zeymer, C.
Funding support Germany, European Union, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 Germany
German Research Foundation (DFG)201302640 Germany
European Research Council (ERC)101039592European Union
German Research Foundation (DFG)453748800 Germany
CitationJournal: Structure / Year: 2025
Title: Modular protein scaffold architecture and AI-guided sequence optimization facilitate de novo metalloenzyme engineering.
Authors: Wagner Egea, P. / Delhommel, F. / Mustafa, G. / Leiss-Maier, F. / Klimper, L. / Badmann, T. / Heider, A. / Wille, I. / Groll, M. / Sattler, M. / Zeymer, C.
History
DepositionApr 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TFD-EH T87E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5099
Polymers18,9441
Non-polymers5658
Water79344
1
A: TFD-EH T87E
hetero molecules

A: TFD-EH T87E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,01918
Polymers37,8882
Non-polymers1,13116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6960 Å2
ΔGint-59 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.360, 76.360, 70.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-203-

IMD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TFD-EH T87E


Mass: 18943.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-M11 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.05 M Imidazole, 14% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 17125 / % possible obs: 96.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.9
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2394 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.765 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21944 856 5 %RANDOM
Rwork0.18969 ---
obs0.19129 16265 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.626 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å2-0 Å2
3---1.76 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 35 44 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131353
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161398
X-RAY DIFFRACTIONr_angle_refined_deg1.191.6231805
X-RAY DIFFRACTIONr_angle_other_deg1.1361.5913207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7085169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54722.98567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40115269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3391510
X-RAY DIFFRACTIONr_chiral_restr0.0480.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
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_it2.2323.524679
X-RAY DIFFRACTIONr_mcbond_other2.2273.518678
X-RAY DIFFRACTIONr_mcangle_it35.279847
X-RAY DIFFRACTIONr_mcangle_other2.9985.286848
X-RAY DIFFRACTIONr_scbond_it2.594.067670
X-RAY DIFFRACTIONr_scbond_other2.5894.069671
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4375.876955
X-RAY DIFFRACTIONr_long_range_B_refined4.28241.6861381
X-RAY DIFFRACTIONr_long_range_B_other4.2441.6021378
X-RAY DIFFRACTIONr_rigid_bond_restr0.8432746
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 65 -
Rwork0.213 1221 -
obs--97.79 %
Refinement TLS params.Method: refined / Origin x: -25.0251 Å / Origin y: 30.2669 Å / Origin z: 5.1914 Å
111213212223313233
T0.0112 Å2-0.0137 Å2-0.0066 Å2-0.0615 Å20.0049 Å2--0.0144 Å2
L0.368 °20.0317 °2-0.1005 °2-0.6702 °2-0.1281 °2--0.4751 °2
S0.0093 Å °0.1126 Å °-0.0017 Å °-0.0346 Å °0.0484 Å °0.0795 Å °0.0407 Å °-0.0731 Å °-0.0576 Å °

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