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- PDB-2wqh: Crystal structure of CTPR3Y3 -

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Basic information

Entry
Database: PDB / ID: 2wqh
TitleCrystal structure of CTPR3Y3
ComponentsCTPR3Y3
KeywordsDE NOVO PROTEIN / MUTANT / TETRATRICOPEPTIDE / TPR DOMAIN
Function / homologyTetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKrachler, A.M. / Sharma, A. / Kleanthous, C.
CitationJournal: Proteins / Year: 2010
Title: Self-association of TPR domains: Lessons learned from a designed, consensus-based TPR oligomer.
Authors: Krachler, A.M. / Sharma, A. / Kleanthous, C.
History
DepositionAug 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_nat
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTPR3Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8745
Polymers14,5131
Non-polymers3604
Water18010
1
A: CTPR3Y3
hetero molecules

A: CTPR3Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,74810
Polymers29,0272
Non-polymers7218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area2600 Å2
ΔGint-21.9 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.284, 62.284, 120.368
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CTPR3Y3


Mass: 14513.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DE NOVO SYNTHESIS / Source: (natural) synthetic construct (others)
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.72 % / Description: NONE
Crystal growpH: 4 / Details: 0.1M MMT PH 4.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 7412 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.61
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4.54 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NA3

1na3


Resolution: 2.2→49.22 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.876 / SU B: 5.541 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL RESIDUES GLY5 AND PRO6 ARE STEROCHEMICALLY REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.28487 343 4.6 %RANDOM
Rwork0.23513 ---
obs0.23733 7068 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.129 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 24 10 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9521303
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0155109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.96926.06661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19715129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02794
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7121.5534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.472840
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3953420
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9934.5463
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 19 -
Rwork0.27 505 -
obs--97.94 %

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