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- PDB-2myf: Solution structure of RNA recognition motif of a cyclophilin33-li... -

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Basic information

Entry
Database: PDB / ID: 2myf
TitleSolution structure of RNA recognition motif of a cyclophilin33-like protein from Plasmodium falciparum
ComponentsRRM containing cyclophilin
KeywordsRNA BINDING PROTEIN / PfCyp33 / RNA recognition motif
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / protein folding / RNA binding / metal ion binding
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
AuthorsGanguly, A.K. / Bhavesh, N.S.
CitationJournal: To be Published
Title: Solution structure of RNA recognition motif of a cyclophilin33-like protein from Plasmodium falciparum
Authors: Ganguly, A.K. / Bhavesh, N.S.
History
DepositionJan 22, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RRM containing cyclophilin


Theoretical massNumber of molelcules
Total (without water)10,1491
Polymers10,1491
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 least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein RRM containing cyclophilin


Mass: 10149.257 Da / Num. of mol.: 1 / Fragment: RNA recognition motif (UNP residues 1-86)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF13_0122 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0H5C7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D C(CO)NH
1813D H(CCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic
11223D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 13C; U-100% 15N] RRM, 20 mM sodium phosphate, 50 mM sodium chloride, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C; U-100% 15N] RRM, 20 mM sodium phosphate, 50 mM sodium chloride, 50 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRRM-1[U-100% 13C; U-100% 15N]0.5-11
20 mMsodium phosphate-21
50 mMsodium chloride-31
50 uMDSS-41
mMRRM-5[U-100% 13C; U-100% 15N]0.5-12
20 mMsodium phosphate-62
50 mMsodium chloride-72
50 uMDSS-82
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1 / Details: WATER REFINEMENT
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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