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- PDB-2m4m: Solution structure of the RRM domain of the hypothetical protein ... -

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Basic information

Entry
Database: PDB / ID: 2m4m
TitleSolution structure of the RRM domain of the hypothetical protein CAGL0M09691g from Candida glabrata
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / THIOREDOXIN-LIKE / New York Structural Genomics Research Consortium / NYSGRC / Nucleocytoplasmic Transport: a Target for Cellular Control / PSI-Biology / NPCXstals
Function / homology
Function and homology information


structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport / nuclear membrane / nucleic acid binding
Similarity search - Function
RNA-recognition motif (RRM) Nup35-type domain / Nucleoporin, NUP53 / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / RRM (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
RRM Nup35-type domain-containing protein
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodSOLUTION NMR / simulating annealing
Model detailslowest energy, model1
AuthorsHarris, R. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Chamala, S. / Evans, B. / Lafleur, J. / Hammonds, J. / Washington, E. / Stead, M. ...Harris, R. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Chamala, S. / Evans, B. / Lafleur, J. / Hammonds, J. / Washington, E. / Stead, M. / Love, J. / Attonito, J. / Patel, H. / Seidel, R.D. / Chook, Y.M. / Rout, M.P. / Girvin, M.E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals)
CitationJournal: To be Published
Title: Solution structure of the RRM domain of the hypothetical protein CAGL0M09691g from Candida glabrata
Authors: Harris, R. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Chamala, S. / Evans, B. / Lafleur, J. / Hammonds, J. / Washington, E. / Stead, M. / Love, J. / Attonito, J. / Patel, H.B. / Seidel, R. ...Authors: Harris, R. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Chamala, S. / Evans, B. / Lafleur, J. / Hammonds, J. / Washington, E. / Stead, M. / Love, J. / Attonito, J. / Patel, H.B. / Seidel, R.D. / Chook, Y.M. / Rout, M.P. / Girvin, M.E. / Almo, S.C.
History
DepositionFeb 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)14,2281
Polymers14,2281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein hypothetical protein /


Mass: 14227.867 Da / Num. of mol.: 1 / Fragment: UNP residues 171-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Strain: CBS 138 / Gene: CAGL0M09691g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FJ27

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC
12115N NOESY-HSQC
13213C HSQC
142aromatic 13C HSQC
15213C NOESY-HSQC
16213C aromatic NOESY-HSQC
171HNCO
181HN(CA)CO
191HNCA
1101HN(CO)CA
1111HN(CA)CB
1121CBCA(CO)NH
NMR detailsText: All 3D experiments were acquired with 30% non-uniform sampling using the MDDNMR approach

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] RRM domain of the hypothetical protein, 10 mM sodium acetate, 100 mM sodium chloride, 0.5 mM DTT, 0.5 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] RRM domain of the hypothetical protein, 10 mM sodium acetate, 100 mM sodium chloride, 0.5 mM DTT, 0.5 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRRM domain of the hypothetical protein-1[U-100% 13C; U-100% 15N]1
10 mMsodium acetate-21
100 mMsodium chloride-31
0.5 mMDTT-41
0.5 mMEDTA-51
1.0 mMRRM domain of the hypothetical protein-6[U-100% 13C; U-100% 15N]2
10 mMsodium acetate-72
100 mMsodium chloride-82
0.5 mMDTT-92
0.5 mMEDTA-102
Sample conditionsIonic strength: 110 / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.refinement
VnmrJ2.2DVariancollection
TopSpin2.1Bruker Biospincollection
MddNMR2.2(MDDNMR) Orekhov, Jaravine, Kazimierczukcollection
MddNMR2.2(MDDNMR) Orekhov, Jaravine, Kazimierczukprocessing
CCPN_Analysis2.2CCPNdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesdata analysis
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHrefinement
RefinementMethod: simulating annealing / Software ordinal: 1 / Details: Refinement in a box of water
NMR constraintsNOE constraints total: 1564 / NOE intraresidue total count: 542 / NOE long range total count: 308 / NOE medium range total count: 261 / NOE sequential total count: 424 / Protein chi angle constraints total count: 12 / Protein phi angle constraints total count: 48 / Protein psi angle constraints total count: 48
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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