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- PDB-8chy: Crystal structure of an 8-repeat consensus TPR superhelix with Zinc. -

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Basic information

Entry
Database: PDB / ID: 8chy
TitleCrystal structure of an 8-repeat consensus TPR superhelix with Zinc.
ComponentsCrystal structure of an 8-repeat consensus TPR superhelix with Zinc.
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: 2 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 8, 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.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: Crystal structure of an 8-repeat consensus TPR superhelix with Zinc.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,42720
Polymers34,1871
Non-polymers1,24019
Water52229
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-333 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.100, 74.100, 238.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-307-

ZN

21A-312-

ZN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Crystal structure of an 8-repeat consensus TPR superhelix with Zinc.


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, 48 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / 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.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 5.5 / Details: 20mM ZnCl2 100mM 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: 1.28195 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: 1.28195 Å / Relative weight: 1
ReflectionResolution: 2→49.92 Å / Num. obs: 27290 / % possible obs: 100 % / Redundancy: 35.9 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rrim(I) all: 0.172 / Net I/σ(I): 14.5 / Num. measured all: 981062
Reflection shellResolution: 2→2.11 Å / % possible obs: 99.9 % / Redundancy: 36.5 % / Num. measured all: 140812 / Num. unique obs: 3862 / CC1/2: 0.734 / Rpim(I) all: 1.427 / Rrim(I) all: 8.666 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.92 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.973 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24869 1285 4.7 %RANDOM
Rwork0.20353 ---
obs0.20568 25891 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 38 29 2363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132386
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171939
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6563243
X-RAY DIFFRACTIONr_angle_other_deg1.5051.584511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02824.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.11915352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.289158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022785
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_it4.4384.9961091
X-RAY DIFFRACTIONr_mcbond_other4.414.9851086
X-RAY DIFFRACTIONr_mcangle_it5.6837.4871357
X-RAY DIFFRACTIONr_mcangle_other5.6877.4881358
X-RAY DIFFRACTIONr_scbond_it6.35.7791295
X-RAY DIFFRACTIONr_scbond_other6.2985.7811296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.6228.4051887
X-RAY DIFFRACTIONr_long_range_B_refined11.11156.2362851
X-RAY DIFFRACTIONr_long_range_B_other11.10956.2552852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 90 -
Rwork0.36 1837 -
obs--99.64 %

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