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- PDB-9qup: Tb(III)-bound de novo protein scaffold TFD-EE MPNN -

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Basic information

Entry
Database: PDB / ID: 9qup
TitleTb(III)-bound de novo protein scaffold TFD-EE MPNN
ComponentsTFD-EE MPNN
KeywordsDE NOVO PROTEIN / TIM barrel / Enzyme Engineering / Metal Coordination / Photoenzyme / ProteinMPNN
Function / homologyTERBIUM(III) ION
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-EE MPNN
B: TFD-EE MPNN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,45913
Polymers36,6772
Non-polymers78211
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-63 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.980, 66.440, 94.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TFD-EE MPNN


Mass: 18338.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-29b+ / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 56 molecules

#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS-HCL, 0.2 M NaCl, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 20002 / % possible obs: 98.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.3
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2681 / % possible all: 96.1

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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: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.432 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22585 999 5 %RANDOM
Rwork0.1959 ---
obs0.1974 18996 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.894 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2--0.73 Å2-0 Å2
3----2.5 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 40 45 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132619
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152710
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.6293522
X-RAY DIFFRACTIONr_angle_other_deg1.0591.5826180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.12420.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81315479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2331530
X-RAY DIFFRACTIONr_chiral_restr0.0330.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
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_it1.1033.5051346
X-RAY DIFFRACTIONr_mcbond_other1.1023.5051345
X-RAY DIFFRACTIONr_mcangle_it1.5565.2561679
X-RAY DIFFRACTIONr_mcangle_other1.5565.2561680
X-RAY DIFFRACTIONr_scbond_it1.0813.8511273
X-RAY DIFFRACTIONr_scbond_other1.0813.8521274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4825.6251844
X-RAY DIFFRACTIONr_long_range_B_refined2.4641.12714
X-RAY DIFFRACTIONr_long_range_B_other2.45241.112714
X-RAY DIFFRACTIONr_rigid_bond_restr0.32635329
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
Rfree0.321 69 -
Rwork0.299 1326 -
obs--95.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13360.02980.07250.1215-0.01610.22990.0053-0.01130.01040.0167-0.00190.01870.0127-0.0227-0.00340.00490.00250.00560.0234-0.00350.027714.43970.733617.9406
20.14690.00720.01950.1713-0.05020.2441-0.0106-0.00430.00810.00460.0067-0.02170.01990.0260.00390.0040.00610.00160.0239-0.00080.028831.2548-0.720712.1019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 169
2X-RAY DIFFRACTION2B1 - 169

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