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- PDB-8cqp: Crystal structure of an 8-repeat consensus TPR superhelix with Ca... -

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Basic information

Entry
Database: PDB / ID: 8cqp
TitleCrystal structure of an 8-repeat consensus TPR superhelix with Calcium (low concentration)
ComponentsMonomer
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: 1.7 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 / 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: Monomer
B: Monomer
C: Monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,76224
Polymers102,5603
Non-polymers1,20221
Water1,62190
1
A: Monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,86013
Polymers34,1871
Non-polymers67312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4235
Polymers34,1871
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Monomer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4796
Polymers34,1871
Non-polymers2935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.448, 70.249, 102.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Monomer


Mass: 34186.594 Da / Num. of mol.: 3
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, 111 molecules

#2: 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
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: CaCl2, 10 mM 100 mM NaOAc, pH 5.5 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.7→70.25 Å / Num. obs: 53530 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rpim(I) all: 0.041 / Rrim(I) all: 0.101 / Net I/σ(I): 7.9 / Num. measured all: 310018
Reflection shellResolution: 1.7→1.79 Å / % possible obs: 100 % / Redundancy: 5.8 % / Num. measured all: 44469 / Num. unique obs: 7724 / CC1/2: 0.477 / Rpim(I) all: 0.571 / Rrim(I) all: 1.392 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALAdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→57.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.975 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23897 2665 5 %RANDOM
Rwork0.20126 ---
obs0.20311 50674 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.298 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→57.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 71 90 3588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133595
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172927
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6584882
X-RAY DIFFRACTIONr_angle_other_deg1.4651.5826807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0195407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33124.667240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11315527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3841511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02808
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_it3.53.9981637
X-RAY DIFFRACTIONr_mcbond_other3.4573.9821624
X-RAY DIFFRACTIONr_mcangle_it4.4345.9592027
X-RAY DIFFRACTIONr_mcangle_other4.4335.9642028
X-RAY DIFFRACTIONr_scbond_it4.5884.5621958
X-RAY DIFFRACTIONr_scbond_other4.5874.5631959
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9846.6582854
X-RAY DIFFRACTIONr_long_range_B_refined8.5244.784265
X-RAY DIFFRACTIONr_long_range_B_other8.5244.7924266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 212 -
Rwork0.336 3656 -
obs--99.33 %

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