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- PDB-9qhb: Crystal structure of 16-repeat CTPR protein with eliminated coord... -

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Basic information

Entry
Database: PDB / ID: 9qhb
TitleCrystal structure of 16-repeat CTPR protein with eliminated coordination sites
ComponentsEngineered tetratricopeptide repeat protein
KeywordsDE NOVO PROTEIN / crystal engineering / protein engineering
Function / homologyACETATE ION
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,91222
Polymers66,5091
Non-polymers1,40321
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-102 kcal/mol
Surface area14380 Å2
Unit cell
Length a, b, c (Å)68.955, 68.955, 148.210
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-604-

CA

21A-711-

HOH

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Components

#1: Protein Engineered tetratricopeptide repeat protein


Mass: 66509.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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

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: 1.969→59.72 Å / Num. obs: 24154 / % possible obs: 81.4 % / Redundancy: 19 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.02 / Rrim(I) all: 0.087 / Net I/σ(I): 17.7
Reflection shellResolution: 1.969→2.109 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.874 / Num. unique obs: 1209 / CC1/2: 0.611 / Rpim(I) all: 0.517 / Rrim(I) all: 1.948

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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: 1.97→59.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.783 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24313 1156 4.8 %RANDOM
Rwork0.19485 ---
obs0.19729 22998 81.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å2-0 Å2
2---0.14 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.97→59.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 83 40 2419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122429
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162126
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.8493294
X-RAY DIFFRACTIONr_angle_other_deg0.5271.7624869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.98958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22210364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
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_it4.0475.1061096
X-RAY DIFFRACTIONr_mcbond_other4.0015.0871087
X-RAY DIFFRACTIONr_mcangle_it5.1069.1111357
X-RAY DIFFRACTIONr_mcangle_other5.1059.1151358
X-RAY DIFFRACTIONr_scbond_it5.745.8181333
X-RAY DIFFRACTIONr_scbond_other5.7385.8171334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.37410.3521938
X-RAY DIFFRACTIONr_long_range_B_refined9.66459.032976
X-RAY DIFFRACTIONr_long_range_B_other9.66459.072968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.02 Å
RfactorNum. reflection% reflection
Rfree0.338 13 -
Rwork0.345 122 -
obs--6.26 %

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