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- PDB-6o33: Crystal Structure Analysis of PIN1 -

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Basic information

Entry
Database: PDB / ID: 6o33
TitleCrystal Structure Analysis of PIN1
Components
  • Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
  • peptide
KeywordsISOMERASE
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 / beta-catenin binding / synapse organization / 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 / 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 / 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
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To be Published
Title: Crystal Structure Analysis of PIN1
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionFeb 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
B: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0023
Polymers18,9062
Non-polymers961
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-11 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.010, 49.010, 137.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 18269.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Protein/peptide peptide


Mass: 636.743 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 45.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 100 mM HEPES, pH 7.2, 3.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2016
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.74→34.66 Å / Num. obs: 18036 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.735 Å2 / Rpim(I) all: 0.045 / Rrim(I) all: 0.161 / Net I/σ(I): 10.3 / Num. measured all: 236222
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all
1.74-1.7713.70.88640.893.32
4.72-34.6611.324.510510.020.068

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PIN

1pin


Resolution: 1.74→34.655 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.71
RfactorNum. reflection% reflection
Rfree0.2375 947 5.27 %
Rwork0.1979 --
obs0.2 17969 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.91 Å2 / Biso mean: 39.7863 Å2 / Biso min: 18.95 Å2
Refinement stepCycle: final / Resolution: 1.74→34.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 5 116 1356
Biso mean--41.68 44.63 -
Num. residues----150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.74-1.83180.33531210.309623722493
1.8318-1.94650.2951260.271623822508
1.9465-2.09680.28321330.229723722505
2.0968-2.30780.26251440.214224032547
2.3078-2.64160.26591280.203724122540
2.6416-3.32780.23611580.19524472605
3.3278-34.66220.1981370.170826342771
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44270.11281.62181.62480.42981.9545-0.0007-0.01920.1692-0.1131-0.1319-0.3506-0.26010.36090.00130.2713-0.0132-0.03310.30920.04070.3093-4.9329-9.526411.9599
20.63070.03780.51751.20020.13230.5085-0.0527-0.37370.22920.5457-0.13970.3576-0.4034-0.1907-0.01410.3482-0.005-0.02930.30910.02910.2717-12.9851-7.70469.3306
30.57260.5637-0.40470.9522-0.05051.4575-0.0857-0.3385-0.72350.1991-0.05190.07410.57240.0207-0.08120.4120.04030.00020.31180.13170.398-10.9918-31.831411.6441
41.28230.4299-0.09042.0237-0.1232.091-0.01540.1522-0.3155-0.3135-0.0791-0.29180.43350.3875-0.01070.34780.0729-0.00620.25990.0660.3396-4.9687-29.38570.451
52.47-0.4832-0.86731.42770.03642.0151-0.0013-0.1504-0.46630.117-0.15990.02320.522-0.0402-0.01020.3485-0.0166-0.01910.26060.09320.3056-14.3947-27.962911.9776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 31 )A6 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 49 )A32 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 72 )A50 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 110 )A73 - 110
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 163 )A111 - 163

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