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- PDB-9quc: Metal-free de novo protein scaffold TFD-EH -

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Basic information

Entry
Database: PDB / ID: 9quc
TitleMetal-free de novo protein scaffold TFD-EH
ComponentsTFD-EH
KeywordsDE NOVO PROTEIN / TIM barrel / Enzyme Engineering / Metal Coordination / Conformational Dynamics
Function / homologyCITRIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4818
Polymers18,9161
Non-polymers5657
Water2,828157
1
A: TFD-EH
hetero molecules

A: TFD-EH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,96116
Polymers37,8322
Non-polymers1,12914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7550 Å2
ΔGint14 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.670, 78.670, 66.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Potassium Citrate, 20% PEG 3350,

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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: Aug 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 31409 / % possible obs: 99.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.3
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5161 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.905 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18393 1569 5 %RANDOM
Rwork0.1568 ---
obs0.15813 29824 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.197 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 37 157 1514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171388
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.6361813
X-RAY DIFFRACTIONr_angle_other_deg1.2141.5883205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61622.87966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67215272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381510
X-RAY DIFFRACTIONr_chiral_restr0.0520.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
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_it1.2423.016683
X-RAY DIFFRACTIONr_mcbond_other1.2393.011682
X-RAY DIFFRACTIONr_mcangle_it1.6544.536852
X-RAY DIFFRACTIONr_mcangle_other1.6534.542853
X-RAY DIFFRACTIONr_scbond_it1.5923.585677
X-RAY DIFFRACTIONr_scbond_other1.5933.589678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.055.173962
X-RAY DIFFRACTIONr_long_range_B_refined3.04138.4151513
X-RAY DIFFRACTIONr_long_range_B_other2.65137.7111480
X-RAY DIFFRACTIONr_rigid_bond_restr0.55332747
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 115 -
Rwork0.235 2195 -
obs--99.74 %

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