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- PDB-8ckr: Crystal structure of an 8-repeat consensus TPR superhelix with in... -

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Basic information

Entry
Database: PDB / ID: 8ckr
TitleCrystal structure of an 8-repeat consensus TPR superhelix with in Hepes with Ca
ComponentsConsensus tetratricopeptide repeat protein
KeywordsDE NOVO PROTEIN / CTPR / polymorphism / metal coordination.
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Consensus tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6639
Polymers34,1871
Non-polymers4778
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-54 kcal/mol
Surface area7800 Å2
Unit cell
Length a, b, c (Å)68.317, 68.317, 72.335
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

21A-479-

HOH

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5 / Details: 20mM CaCl2 100 mM Hepes 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.3→59.17 Å / Num. obs: 48472 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.999 / Rpim(I) all: 0.022 / Rrim(I) all: 0.087 / Net I/σ(I): 11 / Num. measured all: 729150
Reflection shellResolution: 1.3→1.37 Å / % possible obs: 100 % / Redundancy: 14.5 % / Num. measured all: 101260 / Num. unique obs: 6993 / CC1/2: 0.438 / Rpim(I) all: 0.605 / Rrim(I) all: 2.322 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALA7.0.078data scaling
MOSFLM7.2.2data reduction
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→59.16 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.001 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19866 2472 5.1 %RANDOM
Rwork0.1868 ---
obs0.18741 45944 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: 25.941 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.3→59.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 22 94 1264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131215
X-RAY DIFFRACTIONr_bond_other_d0.0010.017996
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.6621657
X-RAY DIFFRACTIONr_angle_other_deg1.6521.5822317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6365139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9324.51282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81815179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.403154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02277
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_it1.8832.418547
X-RAY DIFFRACTIONr_mcbond_other1.8632.416546
X-RAY DIFFRACTIONr_mcangle_it2.6793.624683
X-RAY DIFFRACTIONr_mcangle_other2.693.627684
X-RAY DIFFRACTIONr_scbond_it3.6882.861668
X-RAY DIFFRACTIONr_scbond_other3.6852.865669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5864.158973
X-RAY DIFFRACTIONr_long_range_B_refined6.75828.0741525
X-RAY DIFFRACTIONr_long_range_B_other6.7628.1051526
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 151 -
Rwork0.378 3384 -
obs--99.92 %

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