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- PDB-9qul: Zn(II)-bound de novo protein scaffold TFD-EH T87E -

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Basic information

Entry
Database: PDB / ID: 9qul
TitleZn(II)-bound de novo protein scaffold TFD-EH T87E
ComponentsTFD-EH T87E
KeywordsDE NOVO PROTEIN / TIM barrel / Enzyme Engineering / Metal Coordination / Conformational Dynamics
Function / homologyIMIDAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)19,3256
Polymers18,9441
Non-polymers3815
Water97354
1
A: TFD-EH T87E
hetero molecules

A: TFD-EH T87E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,64912
Polymers37,8882
Non-polymers76210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6810 Å2
ΔGint-93 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.240, 76.240, 70.250
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-

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, 59 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


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


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


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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.05 Imidazole, 16% 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: 1.9→30 Å / Num. obs: 18249 / % possible obs: 96 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / Num. unique obs: 2630 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.628 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21925 912 5 %RANDOM
Rwork0.18149 ---
obs0.18333 17330 96.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.22 Å20 Å2
2--0.43 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 22 55 1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131337
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161379
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.6241786
X-RAY DIFFRACTIONr_angle_other_deg1.1261.593163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5145168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34722.98567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33215265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0121510
X-RAY DIFFRACTIONr_chiral_restr0.0430.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
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_it2.2234.163675
X-RAY DIFFRACTIONr_mcbond_other2.2164.158674
X-RAY DIFFRACTIONr_mcangle_it3.0356.244842
X-RAY DIFFRACTIONr_mcangle_other3.0386.249843
X-RAY DIFFRACTIONr_scbond_it2.5654.687662
X-RAY DIFFRACTIONr_scbond_other2.5644.686663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4456.817945
X-RAY DIFFRACTIONr_long_range_B_refined4.22749.0141375
X-RAY DIFFRACTIONr_long_range_B_other4.22649.0211376
X-RAY DIFFRACTIONr_rigid_bond_restr0.72332715
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 68 -
Rwork0.316 1289 -
obs--98.4 %
Refinement TLS params.Method: refined / Origin x: -24.9352 Å / Origin y: 30.3685 Å / Origin z: 4.9608 Å
111213212223313233
T0.0021 Å2-0.0039 Å2-0.0027 Å2-0.0103 Å20.0009 Å2--0.0456 Å2
L0.0676 °2-0.0657 °2-0.0338 °2-0.1599 °20.027 °2--0.0779 °2
S-0.0024 Å °0.0155 Å °0.0021 Å °-0.0088 Å °0.009 Å °0.01 Å °0.0083 Å °-0.0153 Å °-0.0066 Å °

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