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- PDB-9tsn: ProteinMPNN mutated KREP domain of PF3D7_1343700 (PfK13-KREP, 59,... -

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Basic information

Entry
Database: PDB / ID: 9tsn
TitleProteinMPNN mutated KREP domain of PF3D7_1343700 (PfK13-KREP, 59,4% sequence identity)
ComponentsKelch protein
KeywordsUNKNOWN FUNCTION / Propeller domain / Mutant / Protein Design
Function / homology
Function and homology information


protein homooligomerization
Similarity search - Function
KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Kelch / Kelch repeat type 1 / Kelch-type beta propeller / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / Kelch protein
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsAmann, M. / Straesser, T. / Einsle, O. / Guenther, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)278002225 Germany
CitationJournal: Protein Sci. / Year: 2026
Title: Stabilizing Plasmodium falciparum proteins for small molecule drug discovery.
Authors: Amann, M. / Strasser, T. / Einsle, O. / Gunther, S.
History
DepositionDec 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch protein
B: Kelch protein
C: Kelch protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5146
Polymers102,2403
Non-polymers2743
Water6,756375
1
A: Kelch protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1702
Polymers34,0801
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch protein


Theoretical massNumber of molelcules
Total (without water)34,0801
Polymers34,0801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kelch protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2643
Polymers34,0801
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.428, 92.428, 90.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Kelch protein / Putative kelch protein K13


Mass: 34079.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF13_0238, k13 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A077LQB4
#2: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.8 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.5, 0.5% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.15→90.53 Å / Num. obs: 47058 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.064 / Rrim(I) all: 0.178 / Χ2: 1 / Net I/σ(I): 8.6 / Num. measured all: 357682
Reflection shellResolution: 2.15→2.21 Å / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 1.247 / Num. measured all: 30017 / Num. unique obs: 3866 / CC1/2: 0.677 / Rpim(I) all: 0.475 / Rrim(I) all: 1.335 / Χ2: 1.01 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→80.04 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 2327 4.95 %
Rwork0.1873 --
obs0.1891 47010 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→80.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6718 0 18 375 7111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036948
X-RAY DIFFRACTIONf_angle_d0.6449499
X-RAY DIFFRACTIONf_dihedral_angle_d11.0412486
X-RAY DIFFRACTIONf_chiral_restr0.0511015
X-RAY DIFFRACTIONf_plane_restr0.0061243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.3021050.25642677X-RAY DIFFRACTION100
2.19-2.240.29881300.25992624X-RAY DIFFRACTION100
2.24-2.290.3061280.24932592X-RAY DIFFRACTION100
2.29-2.350.28991500.24572689X-RAY DIFFRACTION100
2.35-2.410.2921280.24382634X-RAY DIFFRACTION100
2.42-2.490.27211240.24822646X-RAY DIFFRACTION100
2.49-2.570.27541360.24552594X-RAY DIFFRACTION100
2.57-2.660.26191440.23822627X-RAY DIFFRACTION100
2.66-2.760.29771860.22172556X-RAY DIFFRACTION100
2.76-2.890.27611330.20972646X-RAY DIFFRACTION100
2.89-3.040.24311580.21522578X-RAY DIFFRACTION100
3.04-3.230.22131500.20352668X-RAY DIFFRACTION100
3.23-3.480.20141310.17472614X-RAY DIFFRACTION100
3.48-3.830.20941580.16622634X-RAY DIFFRACTION100
3.83-4.390.1504970.14382648X-RAY DIFFRACTION100
4.39-5.520.14421420.12842619X-RAY DIFFRACTION100
5.53-80.040.21961270.16912637X-RAY DIFFRACTION100

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