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- PDB-9qui: Ni(II)-bound de novo protein scaffold TFD-EH -

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Basic information

Entry
Database: PDB / ID: 9qui
TitleNi(II)-bound de novo protein scaffold TFD-EH
ComponentsTFD-EH
KeywordsDE NOVO PROTEIN / TIM barrel / Enzyme Engineering / Metal Coordination / Conformational Dynamics
Function / homologyIMIDAZOLE / NICKEL (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)19,3207
Polymers18,9161
Non-polymers4046
Water30617
1
A: TFD-EH
hetero molecules

A: TFD-EH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,64014
Polymers37,8322
Non-polymers80812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7160 Å2
ΔGint-55 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.740, 76.740, 71.210
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


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 , 5 types, 23 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


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


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 17 / 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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.05 M Imidazole, 12% 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: 2.1→30 Å / Num. obs: 13957 / % possible obs: 96.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1826 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.107 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22291 697 5 %RANDOM
Rwork0.18489 ---
obs0.18679 13253 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.826 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.21 Å2-0 Å2
2--0.43 Å20 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 24 17 1352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161387
X-RAY DIFFRACTIONr_angle_refined_deg1.21.6241793
X-RAY DIFFRACTIONr_angle_other_deg1.1111.5913182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5075169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9722.87966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62215268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.821510
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_it3.2555.41679
X-RAY DIFFRACTIONr_mcbond_other3.2545.404678
X-RAY DIFFRACTIONr_mcangle_it4.3178.109847
X-RAY DIFFRACTIONr_mcangle_other4.3168.116848
X-RAY DIFFRACTIONr_scbond_it3.8385.973662
X-RAY DIFFRACTIONr_scbond_other3.8365.974663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8998.71947
X-RAY DIFFRACTIONr_long_range_B_refined5.55362.7011359
X-RAY DIFFRACTIONr_long_range_B_other5.55162.7041359
X-RAY DIFFRACTIONr_rigid_bond_restr0.97732725
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 51 -
Rwork0.295 984 -
obs--98.57 %
Refinement TLS params.Method: refined / Origin x: -25 Å / Origin y: 30.4429 Å / Origin z: 5.1466 Å
111213212223313233
T0.0147 Å2-0.0109 Å2-0.0138 Å2-0.054 Å20.0053 Å2--0.0736 Å2
L0.6807 °2-0.1082 °2-0.1458 °2-0.9456 °20.0681 °2--0.6767 °2
S0.0223 Å °0.1026 Å °-0.0126 Å °-0.0875 Å °-0.0163 Å °0.1235 Å °-0.0063 Å °-0.0933 Å °-0.006 Å °

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