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- PDB-5vtk: Structure of Pin1 WW Domain Variant 1 with beta3-Ser Loop Substitution -

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Basic information

Entry
Database: PDB / ID: 5vtk
TitleStructure of Pin1 WW Domain Variant 1 with beta3-Ser Loop Substitution
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsPROTEIN BINDING / WW domain / beta amino acid
Function / homology
Function and homology information


cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / protein peptidyl-prolyl isomerization / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / : / positive regulation of GTPase activity / ciliary basal body / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / Negative regulators of DDX58/IFIH1 signaling / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / negative regulation of protein catabolic process / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / positive regulation of protein phosphorylation / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...: / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMortenson, D.E. / Kreitler, D.F. / Thomas, N.C. / Gellman, S.H. / Forest, K.T.
CitationJournal: Chembiochem / Year: 2018
Title: Evaluation of beta-Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure.
Authors: Mortenson, D.E. / Kreitler, D.F. / Thomas, N.C. / Guzei, I.A. / Gellman, S.H. / Forest, K.T.
History
DepositionMay 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1865
Polymers4,0451
Non-polymers1424
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-29 kcal/mol
Surface area2930 Å2
Unit cell
Length a, b, c (Å)47.629, 47.629, 60.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

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Components

#1: Protein/peptide Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1


Mass: 4044.538 Da / Num. of mol.: 1 / Fragment: WW domain sequence 1 (UNP residues 6-39) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13526
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 4.3 M sodium chloride (Hampton CSII #36), crystal grew after ~6 months, treated with 4:1 (CS2 #36):glycerol prior to freezing in cryostream

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 0.72 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72 Å / Relative weight: 1
ReflectionResolution: 1.99→34.12 Å / Num. obs: 3112 / % possible obs: 99.7 % / Redundancy: 40.8 % / Biso Wilson estimate: 10.2 Å2 / Rsym value: 0.102 / Net I/σ(I): 38.41
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 24.6 % / Mean I/σ(I) obs: 11.27 / Num. unique obs: 126 / Rsym value: 0.324 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XPREPdata reduction
APEX 2data collection
PHASERphasing
XPREPdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VTJ

5vtj


Resolution: 1.99→34.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.222 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22098 287 9.3 %RANDOM
Rwork0.15685 ---
obs0.1625 2804 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.392 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.99→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms281 0 4 61 346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019309
X-RAY DIFFRACTIONr_bond_other_d0.0030.02284
X-RAY DIFFRACTIONr_angle_refined_deg1.861.93418
X-RAY DIFFRACTIONr_angle_other_deg1.1343653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.794534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7322016
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5011553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.347155
X-RAY DIFFRACTIONr_chiral_restr0.1240.237
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0287
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_it2.0831.172137
X-RAY DIFFRACTIONr_mcbond_other2.0911.151136
X-RAY DIFFRACTIONr_mcangle_it3.4691.697172
X-RAY DIFFRACTIONr_mcangle_other3.4611.721173
X-RAY DIFFRACTIONr_scbond_it2.1581.306172
X-RAY DIFFRACTIONr_scbond_other2.0171.304172
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6191.892246
X-RAY DIFFRACTIONr_long_range_B_refined7.0259.948394
X-RAY DIFFRACTIONr_long_range_B_other6.5429.262372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.991→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 18 -
Rwork0.151 202 -
obs--98.65 %

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