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

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Basic information

Entry
Database: PDB / ID: 2zqt
TitleCrystal structure of a mutant PIN1 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / PIN1 mutant M130A / 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 / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / 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 / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / 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 / postsynaptic cytosol / negative regulation of protein binding / Rho protein signal transduction / regulation of cytokinesis / 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 / beta-catenin binding / negative regulation of protein catabolic process / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / tau protein binding / positive regulation of protein phosphorylation / neuron differentiation / positive regulation of canonical Wnt signaling pathway / 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 / cytoplasm / cytosol
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 / Chitinase A; domain 3 ...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 / Chitinase A; domain 3 / 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 / 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: 1.462 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:
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)18,5603
Polymers18,2111
Non-polymers3482
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.966, 48.966, 138.091
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: 18211.191 Da / Num. of mol.: 1 / Mutation: 'M130A
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.: 179 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
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: 1.46→50 Å / Num. all: 29859 / Num. obs: 29561 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.06 / Net I/σ(I): 11.7

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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: 1.462→30.951 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.2 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.1 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 3461 12.19 %Random
Rwork0.2407 ---
obs0.2442 28402 94.49 %-
all-29859 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.939 Å2 / ksol: 0.418 e/Å3
Displacement parametersBiso max: 69.23 Å2 / Biso mean: 22.293 Å2 / Biso min: 11.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.0333 Å20 Å20 Å2
2--0.0333 Å2-0 Å2
3----0.0667 Å2
Refinement stepCycle: LAST / Resolution: 1.462→30.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 22 179 1410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071254
X-RAY DIFFRACTIONf_angle_d1.1741674
X-RAY DIFFRACTIONf_dihedral_angle_d17.076483
X-RAY DIFFRACTIONf_chiral_restr0.072167
X-RAY DIFFRACTIONf_plane_restr0.006219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4616-1.48160.33151040.2852744X-RAY DIFFRACTION72
1.4816-1.50280.27731240.2511858X-RAY DIFFRACTION84
1.5028-1.52520.34021340.2297904X-RAY DIFFRACTION88
1.5252-1.54910.25811210.235944X-RAY DIFFRACTION92
1.5491-1.57450.25851340.227953X-RAY DIFFRACTION92
1.5745-1.60160.27891300.2117939X-RAY DIFFRACTION92
1.6016-1.63070.2381430.207976X-RAY DIFFRACTION93
1.6307-1.66210.23751370.2175958X-RAY DIFFRACTION94
1.6621-1.6960.24181280.2033984X-RAY DIFFRACTION94
1.696-1.73290.2411250.21341004X-RAY DIFFRACTION96
1.7329-1.77320.25221240.22711023X-RAY DIFFRACTION96
1.7732-1.81750.27181500.2094985X-RAY DIFFRACTION95
1.8175-1.86670.24931490.2124987X-RAY DIFFRACTION96
1.8667-1.92160.22321500.22171005X-RAY DIFFRACTION96
1.9216-1.98360.28421520.22331005X-RAY DIFFRACTION97
1.9836-2.05450.23461190.22681041X-RAY DIFFRACTION97
2.0545-2.13670.26451330.21681025X-RAY DIFFRACTION97
2.1367-2.2340.2281390.22881056X-RAY DIFFRACTION97
2.234-2.35170.24481510.24711006X-RAY DIFFRACTION97
2.3517-2.4990.24271370.2411054X-RAY DIFFRACTION98
2.499-2.69180.27141410.24771059X-RAY DIFFRACTION99
2.6918-2.96250.29491720.26661045X-RAY DIFFRACTION99
2.9625-3.39070.28371320.24491095X-RAY DIFFRACTION99
3.3907-4.27020.23931660.22511095X-RAY DIFFRACTION100
4.2702-30.95750.32981660.26761196X-RAY DIFFRACTION99

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