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- PDB-9qud: Cu(II)-bound de novo protein scaffold TFD-EH -

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Basic information

Entry
Database: PDB / ID: 9qud
TitleCu(II)-bound de novo protein scaffold TFD-EH
ComponentsTFD-EH
KeywordsDE NOVO PROTEIN / TIM barrel / Enzyme Engineering / Metal Coordination / Conformational Dynamics
Function / homologyCOPPER (II) ION / 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

Downloads & links

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Assembly

Deposited unit
A: TFD-EH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,51710
Polymers18,9161
Non-polymers6019
Water1,38777
1
A: TFD-EH
hetero molecules

A: TFD-EH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,03320
Polymers37,8322
Non-polymers1,20118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6750 Å2
ΔGint-25 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.830, 76.830, 70.010
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-202-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TFD-EH


Mass: 18915.980 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 , 6 types, 86 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50 mM Imidazole, 12% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 17755 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 19
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2 / Num. unique obs: 2440 / % possible all: 100

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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: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.741 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21773 887 5 %RANDOM
Rwork0.16626 ---
obs0.16892 16856 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0.35 Å2-0 Å2
2---0.71 Å20 Å2
3---2.3 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 35 77 1423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131353
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161407
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.6311801
X-RAY DIFFRACTIONr_angle_other_deg1.1251.5913226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48722.87966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55115268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7451510
X-RAY DIFFRACTIONr_chiral_restr0.0430.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
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_it2.4374.587679
X-RAY DIFFRACTIONr_mcbond_other2.414.581678
X-RAY DIFFRACTIONr_mcangle_it3.1786.881847
X-RAY DIFFRACTIONr_mcangle_other3.1786.889848
X-RAY DIFFRACTIONr_scbond_it2.6875.247674
X-RAY DIFFRACTIONr_scbond_other2.6865.248675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6827.581955
X-RAY DIFFRACTIONr_long_range_B_refined4.67255.2261417
X-RAY DIFFRACTIONr_long_range_B_other4.62955.0261406
X-RAY DIFFRACTIONr_rigid_bond_restr0.77332757
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 65 -
Rwork0.268 1234 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -25.1775 Å / Origin y: 30.4085 Å / Origin z: 5.1102 Å
111213212223313233
T0.001 Å2-0.0009 Å2-0.0004 Å2-0.0033 Å20.0012 Å2--0.0029 Å2
L0.054 °20.0005 °2-0.0079 °2-0.0836 °20.0065 °2--0.0476 °2
S0.0002 Å °0.0091 Å °-0.0006 Å °-0.0042 Å °0.0033 Å °0.0107 Å °-0.0013 Å °-0.0049 Å °-0.0035 Å °

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