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- PDB-2lo0: Solution structure of the Get5 carboxyl domain from A. fumigatus -

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Basic information

Entry
Database: PDB / ID: 2lo0
TitleSolution structure of the Get5 carboxyl domain from A. fumigatus
ComponentsUncharacterized protein
KeywordsPROTEIN BINDING / dimerization / homodimerization
Function / homologyGet5 carboxyl domain / Get5 dimerization domain / GTP Cyclohydrolase I; Chain A, domain 1 / cytosolic small ribosomal subunit / structural constituent of ribosome / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChartron, J.W. / Vandervelde, D.G. / Rao, M. / Clemons Jr., W.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Get5 Carboxyl-terminal Domain Is a Novel Dimerization Motif That Tethers an Extended Get4/Get5 Complex.
Authors: Chartron, J.W. / Vandervelde, D.G. / Rao, M. / Clemons, W.M.
History
DepositionJan 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Remark 650 HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,5162
Polymers16,5162
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 8258.029 Da / Num. of mol.: 2 / Fragment: carboxyl domain residues 201-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_5G01770 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WE50

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1912D 1H-13C HSQC
11012D 1H-13C HSQC aromatic
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11313D 1H-15N TOCSY
11413D HBHA(CO)NH
11513D H(CCO)NH
11632D 1H-15N HSQC
11722D 1H-15N HSQC
11832D 1H-1H NOESY
11942D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
13.5 mM [U-100% 13C; U-100% 15N] Get5, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
22.5 mM [U-100% 15N] Get5, 20 mM sodium phosphate, 0.02 % sodium azide, 5 % polyacrylamide, 90% H2O/10% D2O90% H2O/10% D2O
32.5 mM [U-100% 15N] Get5, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
44 mM Get5, 2 mM [U-100% 13C; U-100% 15N] Get5, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.5 mMGet5-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
0.02 %sodium azide-31
2.5 mMGet5-4[U-100% 15N]2
20 mMsodium phosphate-52
0.02 %sodium azide-62
5 %polyacrylamide-72
2.5 mMGet5-8[U-100% 15N]3
20 mMsodium phosphate-93
0.02 %sodium azide-103
4 mMGet5-114
2 mMGet5-12[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate-134
0.02 %sodium azide-144
Sample conditionsIonic strength: 50 / pH: 6.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AnalysisCCPNdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
REDCATPrestegarddata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: log-harmonic potential used
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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