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- PDB-5b3y: Crystal structure of hPin1 WW domain (5-23) fused with maltose-bi... -

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Basic information

Entry
Database: PDB / ID: 5b3y
TitleCrystal structure of hPin1 WW domain (5-23) fused with maltose-binding protein
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
KeywordsISOMERASE / SUGAR BINDING PROTEIN
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 / detection of maltose stimulus / maltose transport complex / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / carbohydrate transport / negative regulation of amyloid-beta formation / cytoskeletal motor activity / carbohydrate transmembrane transporter activity / RHO GTPases Activate NADPH Oxidases / maltose binding / phosphoserine residue binding / maltose transport / maltodextrin transmembrane transport / postsynaptic cytosol / negative regulation of protein binding / Rho protein signal transduction / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / regulation of cytokinesis / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / periplasmic space / response to hypoxia / protein stabilization / nuclear speck / ciliary basal body / DNA damage response / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
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. ...: / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Peptidyl-prolyl cis-trans isomerase domain superfamily / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsHanazono, Y. / Takeda, K. / Miki, K.
CitationJournal: Sci Rep / Year: 2016
Title: Structural studies of the N-terminal fragments of the WW domain: Insights into co-translational folding of a beta-sheet protein
Authors: Hanazono, Y. / Takeda, K. / Miki, K.
History
DepositionMar 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2922
Polymers42,9501
Non-polymers3421
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint2 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.296, 57.637, 124.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein


Mass: 42949.590 Da / Num. of mol.: 1
Fragment: UNP(Q13526) residues 5-23,UNP(P0AEX9) residues 27-393
Mutation: R390N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: PIN1, malE / Strain: K-12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, UniProt: P0AEX9
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 27905 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rsym value: 0.084 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 1.901→33.599 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 1401 5.03 %Random selection
Rwork0.1652 ---
obs0.1664 27850 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→33.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 23 416 3409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043066
X-RAY DIFFRACTIONf_angle_d0.7984160
X-RAY DIFFRACTIONf_dihedral_angle_d12.7071129
X-RAY DIFFRACTIONf_chiral_restr0.03452
X-RAY DIFFRACTIONf_plane_restr0.003535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9012-1.96910.22241210.16952594X-RAY DIFFRACTION99
1.9691-2.0480.21741350.16472589X-RAY DIFFRACTION99
2.048-2.14120.2221360.16832600X-RAY DIFFRACTION99
2.1412-2.2540.21061380.17022596X-RAY DIFFRACTION99
2.254-2.39520.21571490.17022600X-RAY DIFFRACTION100
2.3952-2.58010.23471430.17762614X-RAY DIFFRACTION99
2.5801-2.83960.20381490.18312649X-RAY DIFFRACTION100
2.8396-3.25020.17991500.17422668X-RAY DIFFRACTION100
3.2502-4.09380.13691410.14832697X-RAY DIFFRACTION100
4.0938-33.60430.17751390.1562842X-RAY DIFFRACTION100

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