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- PDB-8bu0: Crystal structure of an 8 repeat consensus TPR superhelix with calcium -

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Basic information

Entry
Database: PDB / ID: 8bu0
TitleCrystal structure of an 8 repeat consensus TPR superhelix with calcium
ComponentsConsensus tetratricopeptide repeat protein
KeywordsDE NOVO PROTEIN / CTPR / polymorphism / metal coordination
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionNov 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: 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 / _citation_author.name
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)35,58522
Polymers34,1871
Non-polymers1,39821
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-84 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.428, 67.428, 72.613
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-427-

HOH

21A-481-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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)

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Non-polymers , 5 types, 117 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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, hanging drop / pH: 5.5 / Details: 100 mM NaOAc, pH 5.5, 20 mM CaCl2, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.4→58.4 Å / Num. obs: 37860 / % possible obs: 99.5 % / Redundancy: 17.9 % / CC1/2: 0.999 / Rpim(I) all: 0.018 / Rrim(I) all: 0.08 / Net I/σ(I): 14.2 / Num. measured all: 676928
Reflection shellResolution: 1.4→1.48 Å / % possible obs: 99.8 % / Redundancy: 18 % / Num. measured all: 98822 / Num. unique obs: 5477 / CC1/2: 0.631 / Rpim(I) all: 0.441 / Rrim(I) all: 1.905 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALA3.3.22data scaling
MOSFLM7.4.0data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→45.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.27 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19734 1750 4.6 %RANDOM
Rwork0.18254 ---
obs0.18328 36060 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.692 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.4→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 83 96 1327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171087
X-RAY DIFFRACTIONr_angle_refined_deg1.721.6741741
X-RAY DIFFRACTIONr_angle_other_deg1.5991.5832515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7375145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50524.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42315188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.903155
X-RAY DIFFRACTIONr_chiral_restr0.0990.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02281
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_it2.623.143562
X-RAY DIFFRACTIONr_mcbond_other2.4653.095552
X-RAY DIFFRACTIONr_mcangle_it3.34.651692
X-RAY DIFFRACTIONr_mcangle_other3.2984.651693
X-RAY DIFFRACTIONr_scbond_it4.0373.696719
X-RAY DIFFRACTIONr_scbond_other4.0343.696720
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9775.4091045
X-RAY DIFFRACTIONr_long_range_B_refined6.73435.8121526
X-RAY DIFFRACTIONr_long_range_B_other6.73135.861527
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 112 -
Rwork0.354 2682 -
obs--99.54 %

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