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- PDB-2khz: Solution Structure of RCL -

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Basic information

Entry
Database: PDB / ID: 2khz
TitleSolution Structure of RCL
Componentsc-Myc-responsive protein Rcl
KeywordsNUCLEAR PROTEIN / flexible loop / Nucleus / Phosphoprotein
Function / homology
Function and homology information


Purine catabolism / deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / nucleoside salvage / dGMP catabolic process / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity ...Purine catabolism / deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / nucleoside salvage / dGMP catabolic process / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / identical protein binding / nucleus / cytoplasm
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, distance geometry
Model detailsclosest to the average, model 1
AuthorsDoddapaneni, K. / Mahler, B. / Yuan, C. / Wu, Z.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Solution structure of RCL, a novel 2'-deoxyribonucleoside 5'-monophosphate N-glycosidase
Authors: Doddapaneni, K. / Mahler, B. / Pavlovicz, R. / Haushalter, A. / Yuan, C. / Wu, Z.
History
DepositionApr 15, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: c-Myc-responsive protein Rcl
B: c-Myc-responsive protein Rcl


Theoretical massNumber of molelcules
Total (without water)35,9882
Polymers35,9882
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)15 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein c-Myc-responsive protein Rcl


Mass: 17994.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rcl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O35820

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N TROSY
1223D HNCA
1323D HN(CA)CB
1423D HN(CO)CA
1523D (H)CCH-TOCSY
1623D 1H-15N TOCSY
1722D 1H-13C ct-HSQC
1823D 1H-15N NOESY-TROSY
1933D 1H-13C NOESY-HSQC
11033D 1H-13C-13C HMQC-NOESY-HSQC
11123D 13C-edited NOESY
11223D 15N/13C-filtered 13C-edited NOESY
11312D 1H-15N TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM sodium phosphate, 25 mM sodium chloride, 2 mM DTT, 0.02 % sodium azide-4, 12 % Pf1 phage-5, 90% H2O/10% D2O90% H2O/10% D2O
225 mM sodium phosphate, 25 mM sodium chloride, 2 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
325 mM sodium phosphate, 25 mM sodium chloride, 2 mM DTT-12, 0.02 % sodium azide-13, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMsodium phosphate-11
25 mMsodium chloride-21
2 mMDTT-31
0.02 %sodium azide-41
12 %Pf1 phage-51
25 mMsodium phosphate-62
25 mMsodium chloride-72
2 mMDTT-82
0.02 %sodium azide-92
25 mMsodium phosphate-103
25 mMsodium chloride-113
2 mMDTT-123
0.02 %sodium azide-133
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
ProcheckNMRLaskowski and MacArthurdata analysis
XwinNMRBruker Biospincollection
TopSpinBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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