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- PDB-2zqs: Crystal structure of a mutant PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 2zqs
TitleCrystal structure of a mutant PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / PIN1 mutant / C113A / Cell cycle / Nucleus / Phosphoprotein / Rotamase
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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division ...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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / 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 / postsynaptic cytosol / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / negative regulation of protein binding / positive regulation of GTPase activity / peptidyl-prolyl cis-trans isomerase activity / regulation of cytokinesis / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / negative regulation of ERK1 and ERK2 cascade / regulation of protein stability / negative regulation of protein catabolic process / beta-catenin binding / ISG15 antiviral mechanism / tau protein binding / neuron differentiation / positive regulation of canonical Wnt signaling pathway / positive regulation of protein phosphorylation / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / ciliary basal body / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / 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 / Chitinase A; domain 3 - #40 / WW domain ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / 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 / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / Chitinase A; domain 3 / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Single Sheet / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsJobichen, C. / Liou, Y.C. / Sivaraman, J.
CitationJournal: To be Published
Title: Structural studies on PIN1 mutants
Authors: Jobichen, C. / Liou, Y.C. / Sivaraman, J.
History
DepositionAug 19, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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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)18,5883
Polymers18,2391
Non-polymers3482
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.758, 48.758, 137.980
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 Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / Rotamase Pin1 / PPIase Pin1


Mass: 18239.244 Da / Num. of mol.: 1 / Mutation: C113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2006
RadiationMonochromator: CN1707 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.902→50 Å / Num. obs: 13863 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29.21 Å2 / Rsym value: 0.073 / Net I/σ(I): 8.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PIN

1pin


Resolution: 1.902→30.84 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1617 12.38 %RANDOM
Rwork0.2377 ---
all0.2436 13863 --
obs0.2377 13062 94.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.474 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 85.02 Å2 / Biso mean: 34.273 Å2 / Biso min: 17.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.576 Å20 Å2-0 Å2
2--1.576 Å20 Å2
3----3.151 Å2
Refinement stepCycle: LAST / Resolution: 1.902→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 22 129 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051237
X-RAY DIFFRACTIONf_angle_d0.8481657
X-RAY DIFFRACTIONf_chiral_restr0.06166
X-RAY DIFFRACTIONf_plane_restr0.004220
X-RAY DIFFRACTIONf_dihedral_angle_d17.143472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.902-1.9580.2941100.21782093083
1.958-2.0210.3091030.21989399689
2.021-2.0930.3021410.219891103291
2.093-2.1770.2731070.224928103593
2.177-2.2760.2991270.217944107195
2.276-2.3960.2581390.229912105193
2.396-2.5460.2751520.228943109595
2.546-2.7420.2991350.238970110597
2.742-3.0180.3051360.2581001113798
3.018-3.4540.3121430.2531004114798
3.454-4.350.2471570.2071018117599
4.35-30.8440.2871670.24911211288100

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