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- PDB-4gwt: Structure of racemic Pin1 WW domain cocrystallized with DL-malic acid -

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Basic information

Entry
Database: PDB / ID: 4gwt
TitleStructure of racemic Pin1 WW domain cocrystallized with DL-malic acid
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsPROTEIN BINDING / racemic crystallization / WW domain / proline phosphoSer/Thr 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
(2S)-2-hydroxybutanedioic acid / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMortenson, D.E. / Yun, H.G. / Gellman, S.H. / Forest, K.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Evidence for small-molecule-mediated loop stabilization in the structure of the isolated Pin1 WW domain.
Authors: Mortenson, D.E. / Kreitler, D.F. / Yun, H.G. / Gellman, S.H. / Forest, K.T.
History
DepositionSep 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)4,3092
Polymers4,1751
Non-polymers1341
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.985, 65.985, 38.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number88
Space group name H-MI41/a

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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: 4174.641 Da / Num. of mol.: 1 / Fragment: WW domain from Pin1, (6-39) / Source method: obtained synthetically / Details: Generated via solid-phase peptide synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Peptide stock at 5 mg/mL (2.5 mg/mL L-peptide + 2.5 mg/L D-peptide), crystallized from 2.1 M DL-malic acid pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 30, 2011
RadiationMonochromator: Bruker Microstar AXS optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→33.32 Å / Num. all: 4031 / Num. obs: 4031 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 41.6 Å2 / Rsym value: 0.069 / Χ2: 0.989 / Net I/σ(I): 22.85
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueΧ2Diffraction-ID% possible all
2.25-2.299.11900.290.8971100
2.29-2.3310.71910.3630.9751100
2.33-2.38122010.2580.9021100
2.38-2.4213.62110.2150.9571100
2.42-2.4813.81990.1950.8911100
2.48-2.5313.82060.1820.9761100
2.53-2.613.51880.1640.9651100
2.6-2.67142020.1630.9771100
2.67-2.7513.22070.1171.0681100
2.75-2.8313.91960.1151.0551100
2.83-2.9413.71990.0981.0441100
2.94-3.05141950.0771.0921100
3.05-3.1914.12090.0711.0561100
3.19-3.3614.12050.0630.9881100
3.36-3.5714.21930.0571.0511100
3.57-3.8514.12070.0551.0621100
3.85-4.23142070.0520.8981100
4.23-4.8514.11990.0510.9221100
4.85-6.113.92050.0490.9851100
6.1-5012.82210.0820.962199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0009refinement
PDB_EXTRACT3.11data extraction
PROTEUM PLUSPLUSdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IDH, CORE BETA-SHEET FRAGMENT (RESI 260-263,268-272,277-279)

2idh


Resolution: 2.25→33.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.765 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 172 4.5 %RANDOM
Rwork0.2384 ---
all0.2393 4029 --
obs0.2394 3857 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.34 Å2 / Biso mean: 39.5828 Å2 / Biso min: 21.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å2-0 Å2
3---0.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.168 Å0.086 Å
Refinement stepCycle: LAST / Resolution: 2.25→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms276 0 9 11 296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019294
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.933397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.041532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.88420.66715
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6871544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.693154
X-RAY DIFFRACTIONr_chiral_restr0.070.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022237
LS refinement shellResolution: 2.25→2.371 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 25 -
Rwork0.348 527 -
all-552 -
obs--99.82 %

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