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- PDB-2jv4: Structure Characterisation of PINA WW Domain and Comparison with ... -

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Basic information

Entry
Database: PDB / ID: 2jv4
TitleStructure Characterisation of PINA WW Domain and Comparison with other Group IV WW Domains, PIN1 and ESS1
ComponentsPeptidyl-prolyl cis/trans isomerase
KeywordsISOMERASE / PPIASE DOMAIN / WW DOMAIN GROUP IV / Rotamase
Function / homology
Function and homology information


regulation of macromolecule metabolic process / regulation of primary metabolic process / membrane => GO:0016020 / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / transferase activity
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / 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. ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / 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 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsMinimisation of the 20 NMR conformers with NMR constraints.
AuthorsNg, C.A. / Kato, Y. / Tanokura, M. / Brownlee, R.T.C.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Structural characterisation of PinA WW domain and a comparison with other Group IV WW domains, Pin1 and Ess1
Authors: Ng, C.A. / Kato, Y. / Tanokura, M. / Brownlee, R.T.C.
History
DepositionSep 11, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
SupersessionOct 23, 2007ID: 2JM7
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis/trans isomerase


Theoretical massNumber of molelcules
Total (without water)6,2571
Polymers6,2571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl-prolyl cis/trans isomerase


Mass: 6256.968 Da / Num. of mol.: 1 / Fragment: WW Domain, Residues UNP 1-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: pinA / Plasmid: PLYSS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O42735, UniProt: Q5AZY5*PLUS, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Minimisation of the 20 NMR conformers with NMR constraints.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNHA
1213D 13C- SEPARATED NOESY
1313D 15N- SEPARATED NOESY
1412D 1H-15N HSQC
1513D HN(CA)CB
1613D HN(COCA)CB
1713D (H)CCH-COSY
1813D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1.8mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS/TRANS ISOMERASE, 50mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.8 mMPEPTIDYL-PROLYL CIS/TRANS ISOMERASE[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate1
50 mMsodium chloride1
0.02 %sodium azide1
Sample conditionsIonic strength: 0.2 / pH: 5 / Pressure: AMBIENT / Temperature: 283 K

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NMR measurement

NMR spectrometerType: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddardchemical shift assignment
Sparky3Goddarddata analysis
Sparky3Goddardpeak picking
VNMRVariancollection
TALOSCornilescu, Delaglio and Baxdihedral angle
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollrefinement
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollenergy minimisation
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: ENERGY MINIMISASTION SUBJECT TO NMR CONSTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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