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- PDB-1f8a: STRUCTURAL BASIS FOR THE PHOSPHOSERINE-PROLINE RECOGNITION BY GRO... -

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Basic information

Entry
Database: PDB / ID: 1f8a
TitleSTRUCTURAL BASIS FOR THE PHOSPHOSERINE-PROLINE RECOGNITION BY GROUP IV WW DOMAINS
Components
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1
  • Y(SEP)PT(SEP)S PEPTIDE
KeywordsISOMERASE / Peptidyl-Proline Isomerase / WW domain / phosphoserine 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 / negative regulation of protein binding / regulation of cytokinesis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / synapse organization / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / negative regulation of ERK1 and ERK2 cascade / negative regulation of protein catabolic process / neuron differentiation / 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 / response to hypoxia / protein stabilization / 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
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. ...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. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / Chitinase A; domain 3 / 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 / Resolution: 1.84 Å
AuthorsVerdecia, M.A. / Bowman, M.E. / Lu, K.P. / Hunter, T. / Noel, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis for phosphoserine-proline recognition by group IV WW domains.
Authors: Verdecia, M.A. / Bowman, M.E. / Lu, K.P. / Hunter, T. / Noel, J.P.
History
DepositionJun 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2013Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1
C: Y(SEP)PT(SEP)S PEPTIDE


Theoretical massNumber of molelcules
Total (without water)19,5082
Polymers19,5082
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.270, 43.903, 124.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer of Pin1 bound to the phosphorylated peptide

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 / PIN1


Mass: 18610.641 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) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Protein/peptide Y(SEP)PT(SEP)S PEPTIDE


Mass: 897.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SOLID-PHASE PEPTIDE SYNTHESIS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MOPSO-Na+, 28% PEG 8000, 2 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMOPSO-Na+1reservoir
228 %(v/v)PEG80001reservoir
32 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MACSCIENCE DIP100S / Detector: IMAGE PLATE / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→62.02 Å / Num. obs: 293095 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.5
Reflection shellResolution: 1.84→1.9 Å / Rmerge(I) obs: 0.337 / Num. unique all: 17107 / % possible all: 98.2
Reflection
*PLUS
Num. obs: 17107 / Num. measured all: 293095
Reflection shell
*PLUS
% possible obs: 98.2 % / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.84→41.41 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1085629.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 866 5.1 %RANDOM
Rwork0.231 ---
obs0.231 17107 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36 Å2 / ksol: 0.3734 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20 Å2
2--3.3 Å20 Å2
3----5.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 152 1446
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.029
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d1.48
X-RAY DIFFRACTIONc_mcbond_it0.851.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it1.442
X-RAY DIFFRACTIONc_scangle_it2.042.5
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 147 5.4 %
Rwork0.239 2555 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.029
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.48
X-RAY DIFFRACTIONc_mcbond_it0.851.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.239

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