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- PDB-8ot7: Crystal structure of an 8-repeat consensus TPR superhelix with Barium -

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Basic information

Entry
Database: PDB / ID: 8ot7
TitleCrystal structure of an 8-repeat consensus TPR superhelix with Barium
ComponentsConsensus tetratricopeptide repeat protein
KeywordsDE NOVO PROTEIN / CTPR / polymorphism / metal coordination.
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLiutkus, M. / Rojas, A.L. / Cortajarena, A.L.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ProNANO- 648071European Union
CitationJournal: Protein Sci. / Year: 2024
Title: Diverse crystalline protein scaffolds through metal-dependent polymorphism.
Authors: Liutkus, M. / Sasselli, I.R. / Rojas, A.L. / Cortajarena, A.L.
History
DepositionApr 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Consensus tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2859
Polymers34,1871
Non-polymers1,0998
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-40 kcal/mol
Surface area14910 Å2
Unit cell
Length a, b, c (Å)70.237, 70.237, 73.568
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Consensus tetratricopeptide repeat protein


Mass: 34186.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20mM BaCl2 100 mM NaOAc, pH 5.5 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 2.36296 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.36296 Å / Relative weight: 1
ReflectionResolution: 3.3→73.56 Å / Num. obs: 6121 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.962 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.063 / Rrim(I) all: 0.185 / Net I/σ(I): 5.5 / Num. measured all: 49097
Reflection shellResolution: 3.3→3.48 Å / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.831 / Num. measured all: 6877 / Num. unique obs: 898 / CC1/2: 0.567 / Rpim(I) all: 0.336 / Rrim(I) all: 0.946 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→60.83 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.911 / SU B: 41.605 / SU ML: 0.608 / Cross valid method: THROUGHOUT / ESU R Free: 0.636 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29877 350 5.7 %RANDOM
Rwork0.18661 ---
obs0.19314 5754 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 141.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 3.3→60.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 8 0 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122367
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181914
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6543221
X-RAY DIFFRACTIONr_angle_other_deg1.3041.5814460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.745271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91924.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.44115352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.876158
X-RAY DIFFRACTIONr_chiral_restr0.0640.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022769
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02543
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_it14.4815.0411087
X-RAY DIFFRACTIONr_mcbond_other14.4415.041086
X-RAY DIFFRACTIONr_mcangle_it22.07422.5311357
X-RAY DIFFRACTIONr_mcangle_other22.07122.5351358
X-RAY DIFFRACTIONr_scbond_it12.72315.6231280
X-RAY DIFFRACTIONr_scbond_other12.7115.6241280
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.97323.2321865
X-RAY DIFFRACTIONr_long_range_B_refined26.33410181
X-RAY DIFFRACTIONr_long_range_B_other26.33510180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 14 -
Rwork0.412 453 -
obs--100 %

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