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- PDB-8cqq: Crystal structure of an 8-repeat consensus TPR superhelix with Copper -

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Basic information

Entry
Database: PDB / ID: 8cqq
TitleCrystal structure of an 8-repeat consensus TPR superhelix with Copper
ComponentsConsensus tetratricopeptide repeat protein
KeywordsDE NOVO PROTEIN / CTPR / polymorphism / metal coordination.
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionMar 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 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.year / _citation_author.identifier_ORCID / _citation_author.name

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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)34,6987
Polymers34,1871
Non-polymers5116
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-81 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.450, 55.450, 55.520
Angle α, β, γ (deg.)111.47, 111.13, 105.80
Int Tables number1
Space group name H-MP1

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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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 10 mM CuSO4 100 mM NaOAc 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.37323 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37323 Å / Relative weight: 1
ReflectionResolution: 2.6→45.77 Å / Num. obs: 14716 / % possible obs: 94.1 % / Redundancy: 2.7 % / CC1/2: 0.959 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.107 / Rrim(I) all: 0.185 / Net I/σ(I): 5.3 / Num. measured all: 39734
Reflection shellResolution: 2.6→2.74 Å / % possible obs: 92.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.548 / Num. measured all: 5632 / Num. unique obs: 2115 / CC1/2: 0.546 / Rpim(I) all: 0.432 / Rrim(I) all: 0.751 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.895 / SU B: 8.652 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26124 783 5.3 %RANDOM
Rwork0.17778 ---
obs0.18198 13913 94.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.493 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20.41 Å20.06 Å2
2--0.86 Å2-0.87 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 2.6→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 22 8 2327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132384
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181914
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6543247
X-RAY DIFFRACTIONr_angle_other_deg1.3461.5814460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6235271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60224.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.21715352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.149158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
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_it2.9374.7141087
X-RAY DIFFRACTIONr_mcbond_other2.9374.7091086
X-RAY DIFFRACTIONr_mcangle_it4.6847.0691357
X-RAY DIFFRACTIONr_mcangle_other4.6837.0751358
X-RAY DIFFRACTIONr_scbond_it4.6485.561297
X-RAY DIFFRACTIONr_scbond_other4.665.4651280
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6977.9511866
X-RAY DIFFRACTIONr_long_range_B_refined11.67789.63410186
X-RAY DIFFRACTIONr_long_range_B_other11.67789.58610182
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 53 -
Rwork0.242 1019 -
obs--91.78 %

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