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- PDB-8ch0: Crystal structure of an 8-repeat consensus TPR superhelix with Ga... -

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Basic information

Entry
Database: PDB / ID: 8ch0
TitleCrystal structure of an 8-repeat consensus TPR superhelix with Gadolinium.
ComponentsConsensus tetratricopeptide repeat protein
KeywordsDE NOVO PROTEIN / CTPR / polymorphism / metal coordination
Function / homologyGADOLINIUM ATOM
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 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

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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)17,3857
Polymers16,5551
Non-polymers8306
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-33 kcal/mol
Surface area7910 Å2
Unit cell
Length a, b, c (Å)44.228, 57.730, 76.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Consensus tetratricopeptide repeat protein


Mass: 16554.691 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-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8 / Details: 5mM GdCl3 100 mM Tris HCl 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.711822 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2020 / Details: Elliptically bent mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.711822 Å / Relative weight: 1
ReflectionResolution: 1.75→57.73 Å / Num. obs: 20384 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.997 / Rpim(I) all: 0.031 / Rrim(I) all: 0.106 / Net I/σ(I): 13.2 / Num. measured all: 234292
Reflection shellResolution: 1.75→1.84 Å / % possible obs: 100 % / Redundancy: 11 % / Num. measured all: 32240 / Num. unique obs: 2930 / CC1/2: 0.958 / Rpim(I) all: 0.207 / Rrim(I) all: 0.687 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
XSCALEdata scaling
autoPROCdata reduction
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.03 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.466 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20984 902 4.4 %RANDOM
Rwork0.17873 ---
obs0.18005 19398 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.778 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å20 Å20 Å2
2---2.45 Å20 Å2
3----2.69 Å2
Refinement stepCycle: 1 / Resolution: 1.75→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 27 49 1224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131204
X-RAY DIFFRACTIONr_bond_other_d0.0020.017994
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.661638
X-RAY DIFFRACTIONr_angle_other_deg1.5541.5852308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88824.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12515176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.455154
X-RAY DIFFRACTIONr_chiral_restr0.1140.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
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_it3.2633.73544
X-RAY DIFFRACTIONr_mcbond_other3.263.728542
X-RAY DIFFRACTIONr_mcangle_it4.095.566677
X-RAY DIFFRACTIONr_mcangle_other4.0895.569678
X-RAY DIFFRACTIONr_scbond_it5.3294.386660
X-RAY DIFFRACTIONr_scbond_other5.3254.389661
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9176.346962
X-RAY DIFFRACTIONr_long_range_B_refined8.54842.1551451
X-RAY DIFFRACTIONr_long_range_B_other8.54642.1861452
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 60 -
Rwork0.335 1400 -
obs--99.46 %

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