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- PDB-9qhc: Crystal structure of 8-repeat CTPR protein with eliminated coordi... -

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Basic information

Entry
Database: PDB / ID: 9qhc
TitleCrystal structure of 8-repeat CTPR protein with eliminated coordination sites
ComponentsEngineered tetratricopeptide repeat protein
KeywordsDE NOVO PROTEIN / crystal engineering / protein engineering
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsLiutkus, M. / Rojas, A.L. / Cortajarena, A.L.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)863170European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Rational Crystal Contact Engineering for Programmable Self-Assembled Protein Architectures.
Authors: Liutkus, M. / Rojas, A.L. / Cortajarena, A.L.
History
DepositionMar 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engineered tetratricopeptide repeat protein
B: Engineered tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6995
Polymers68,5002
Non-polymers1983
Water905
1
A: Engineered tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4083
Polymers34,2501
Non-polymers1582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Engineered tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2902
Polymers34,2501
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.260, 134.185, 78.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Engineered tetratricopeptide repeat protein


Mass: 34250.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium acetate, pH 5.5, 100 mM CaCl2, 25% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.879→67.18 Å / Num. obs: 10700 / % possible obs: 54.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.023 / Rrim(I) all: 0.08 / Net I/σ(I): 16.3
Reflection shellResolution: 2.879→3.216 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.38 / Num. unique obs: 535 / CC1/2: 0.673 / Rpim(I) all: 0.446 / Rrim(I) all: 1.454

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimless0.7.4data scaling
XDSdata reduction
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→67.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.832 / SU B: 24.757 / SU ML: 0.476 / Cross valid method: THROUGHOUT / ESU R Free: 0.818 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33834 520 4.9 %RANDOM
Rwork0.20552 ---
obs0.21195 10180 54.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.651 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2---0.53 Å20 Å2
3----1.26 Å2
Refinement stepCycle: 1 / Resolution: 2.88→67.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 10 5 4654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124788
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164125
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.8446505
X-RAY DIFFRACTIONr_angle_other_deg0.5321.7689493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.964515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.9310738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025827
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021217
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_it9.339.7062206
X-RAY DIFFRACTIONr_mcbond_other9.3219.7042206
X-RAY DIFFRACTIONr_mcangle_it14.79817.4162754
X-RAY DIFFRACTIONr_mcangle_other14.80117.4192755
X-RAY DIFFRACTIONr_scbond_it8.83310.6232582
X-RAY DIFFRACTIONr_scbond_other8.83110.6222583
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.56719.1933752
X-RAY DIFFRACTIONr_long_range_B_refined20.477110.956229
X-RAY DIFFRACTIONr_long_range_B_other20.475110.946230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.88→2.954 Å
RfactorNum. reflection% reflection
Rfree0.792 4 -
Rwork0.569 55 -
obs--4.19 %

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