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- PDB-8cp8: Crystal structure of an 8-repeat consensus TPR superhelix with Lead -

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Basic information

Entry
Database: PDB / ID: 8cp8
TitleCrystal structure of an 8-repeat consensus TPR superhelix with Lead
ComponentsConsensus tetratricopeptide repeat protein
KeywordsDE NOVO PROTEIN / CTPR / polymorphism / metal coordination.
Function / homologyACETATE ION / LEAD (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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

Downloads & links

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Assembly

Deposited unit
A: Consensus tetratricopeptide repeat protein
B: Consensus tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,83948
Polymers68,3732
Non-polymers4,46646
Water1,78399
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A: Consensus tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,74828
Polymers34,1871
Non-polymers2,56127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Consensus tetratricopeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,09120
Polymers34,1871
Non-polymers1,90519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.257, 73.257, 117.609
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-420-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Consensus tetratricopeptide repeat protein


Mass: 34186.594 Da / Num. of mol.: 2
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, 145 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: 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
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Pb / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

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, hanging drop / pH: 5.5 / Details: 100mM NaOAc 20mM PbCl2 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.951147 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: 0.951147 Å / Relative weight: 1
ReflectionResolution: 1.68→117.609 Å / Num. obs: 42074 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.065 / Rrim(I) all: 0.284 / Net I/σ(I): 6.9
Reflection shellResolution: 1.684→1.713 Å / Redundancy: 17.1 % / Rmerge(I) obs: 3.89 / Mean I/σ(I) obs: 1 / Num. unique obs: 2098 / CC1/2: 0.701 / Rpim(I) all: 0.952 / Rrim(I) all: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
autoPROCdata scaling
autoPROCdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→55.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.771 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23401 2166 5.2 %RANDOM
Rwork0.204 ---
obs0.20555 39859 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.68→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 105 99 2500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132437
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172005
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.6643292
X-RAY DIFFRACTIONr_angle_other_deg1.1981.5824647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9885270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77924.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06815352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.817158
X-RAY DIFFRACTIONr_chiral_restr0.0530.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
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_it1.163.561094
X-RAY DIFFRACTIONr_mcbond_other1.163.5451088
X-RAY DIFFRACTIONr_mcangle_it1.9155.3041354
X-RAY DIFFRACTIONr_mcangle_other1.9145.3081355
X-RAY DIFFRACTIONr_scbond_it2.3893.8611343
X-RAY DIFFRACTIONr_scbond_other1.4683.8541332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4165.7091939
X-RAY DIFFRACTIONr_long_range_B_refined5.21540.4012949
X-RAY DIFFRACTIONr_long_range_B_other4.98839.9482920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.684→1.728 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 149 -
Rwork0.342 2915 -
obs--99.97 %

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