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- PDB-5vti: Structure of Pin1 WW Domain Sequence 3 with [R,R]-ACPC Loop Subst... -

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Basic information

Entry
Database: PDB / ID: 5vti
TitleStructure of Pin1 WW Domain Sequence 3 with [R,R]-ACPC Loop Substitution
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsPROTEIN BINDING / beta amino acid / WW domain / phosphopeptide binding
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 / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / 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 / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ciliary basal body / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / synapse organization / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein stability / tau protein binding / neuron differentiation / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / protein stabilization / response to hypoxia / nuclear speck / positive regulation of protein phosphorylation / cell cycle / 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. / Domain with 2 conserved Trp (W) residues ...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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)3,8462
Polymers3,8101
Non-polymers351
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area2720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.173, 48.173, 37.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 3810.305 Da / Num. of mol.: 1 / Fragment: WW domain sequence 3 (UNP residues 6-39) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13526
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris, pH 8.5, 3.0 M sodium chloride (Hampton Index #12), cryoprotection: dragged through Paratone-N prior to freezing

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.8→48.17 Å / Num. obs: 4398 / % possible obs: 99.9 % / Redundancy: 26.4 % / Biso Wilson estimate: 31.6 Å2 / Rpim(I) all: 0.015 / Rsym value: 0.076 / Net I/σ(I): 25.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 28.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 617 / Rpim(I) all: 0.36 / Rsym value: 1.902 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4GWT

4gwt


Resolution: 1.8→34.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.466 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27491 406 9.3 %RANDOM
Rwork0.2307 ---
obs0.235 3963 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.8→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms265 0 1 42 308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019303
X-RAY DIFFRACTIONr_bond_other_d0.0030.02276
X-RAY DIFFRACTIONr_angle_refined_deg1.711.946415
X-RAY DIFFRACTIONr_angle_other_deg0.9393636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.899534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58421.2516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7011550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.119154
X-RAY DIFFRACTIONr_chiral_restr0.1020.237
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0284
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_it1.7292.9134
X-RAY DIFFRACTIONr_mcbond_other1.6382.883133
X-RAY DIFFRACTIONr_mcangle_it2.7674.329170
X-RAY DIFFRACTIONr_mcangle_other2.7694.344171
X-RAY DIFFRACTIONr_scbond_it1.2963.014169
X-RAY DIFFRACTIONr_scbond_other1.2923.014169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.274.442245
X-RAY DIFFRACTIONr_long_range_B_refined7.0524.06361
X-RAY DIFFRACTIONr_long_range_B_other6.923.134350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 25 -
Rwork0.298 290 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -6.1964 Å / Origin y: 14.1703 Å / Origin z: -0.2445 Å
111213212223313233
T0.0581 Å2-0.0237 Å20.0283 Å2-0.0606 Å2-0.0172 Å2--0.1053 Å2
L5.0692 °21.2973 °2-2.5331 °2-4.2561 °2-0.2896 °2--6.313 °2
S-0.3813 Å °-0.0298 Å °-0.5493 Å °-0.1981 Å °-0.0418 Å °0.1671 Å °0.2972 Å °-0.0927 Å °0.423 Å °

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