BMRB Entry 16258

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16258
MolProbity Validation Chart

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Title:
Solution Structure of RCL
Deposition date:
2009-04-15
Original release date:
2009-09-04
Authors:
Doddapaneni, K.; Mahler, B; Yuan, C.; Wu, Z.
Citation:

Citation: Doddapaneni, Kiran; Mahler, Bryon; Pavlovicz, Ryan; Haushalter, Adam; Yuan, Chunhua; Wu, Zhengrong. "Solution structure of RCL, a novel 2'-deoxyribonucleoside 5'-monophosphate N-glycosidase."  J. Mol. Biol. 394, 423-434 (2009).
PubMed: 19720067

Assembly members:

Assembly members:
RCL, polymer, 165 residues, 17799.068 Da.

Natural source:

Natural source:   Common Name: Rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET24d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RCL: GHMAASGEQAPCSVYFCGSI RGGREDQALYARIVSRLRRY GKVLTEHVADAELEPLGEEA AGGDQFIHEQDLNWLQQADV VVAEVTQPSLGVGYELGRAV ALGKPILCLFRPQSGRVLSA MIRGAADGSRFQVWDYAEGE VETMLDRYFEAYLPQKTASS SHPSA

Data sets:
Data typeCount
13C chemical shifts634
15N chemical shifts146
1H chemical shifts899

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1RCL_11
2RCL_21

Entities:

Entity 1, RCL_1 165 residues - 17799.068 Da.

1   GLYHISMETALAALASERGLYGLUGLNALA
2   PROCYSSERVALTYRPHECYSGLYSERILE
3   ARGGLYGLYARGGLUASPGLNALALEUTYR
4   ALAARGILEVALSERARGLEUARGARGTYR
5   GLYLYSVALLEUTHRGLUHISVALALAASP
6   ALAGLULEUGLUPROLEUGLYGLUGLUALA
7   ALAGLYGLYASPGLNPHEILEHISGLUGLN
8   ASPLEUASNTRPLEUGLNGLNALAASPVAL
9   VALVALALAGLUVALTHRGLNPROSERLEU
10   GLYVALGLYTYRGLULEUGLYARGALAVAL
11   ALALEUGLYLYSPROILELEUCYSLEUPHE
12   ARGPROGLNSERGLYARGVALLEUSERALA
13   METILEARGGLYALAALAASPGLYSERARG
14   PHEGLNVALTRPASPTYRALAGLUGLYGLU
15   VALGLUTHRMETLEUASPARGTYRPHEGLU
16   ALATYRLEUPROGLNLYSTHRALASERSER
17   SERHISPROSERALA

Samples:

Aniso_water: sodium phosphate 25 mM; sodium chloride 25 mM; DTT 2 mM; sodium azide 0.02%; Pf1 phage 12%

Iso_water: sodium phosphate 25 mM; sodium chloride 25 mM; DTT 2 mM; sodium azide 0.02%

D20: sodium phosphate 25 mM; sodium chloride 25 mM; DTT 2 mM; sodium azide 0.02%

sample_conditions_1: pH: 6.5; pressure: 1.0 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYIso_waterisotropicsample_conditions_1
3D HNCAIso_waterisotropicsample_conditions_1
3D HNCACBIso_waterisotropicsample_conditions_1
3D HNCOCAIso_waterisotropicsample_conditions_1
3D HCCH-TOCSYIso_waterisotropicsample_conditions_1
3D 1H-15N TOCSYIso_waterisotropicsample_conditions_1
2D 1H-13C ct-HSQCIso_waterisotropicsample_conditions_1
3D 1H-15N NOESY-TROSYIso_waterisotropicsample_conditions_1
3D 1H-13C NOESY-HSQCD20isotropicsample_conditions_1
3D 1H-13C-13C HMQC-NOESY-HSQCD20isotropicsample_conditions_1
3D 13C-edited NOESYIso_waterisotropicsample_conditions_1
3D 15N/13C-filtered 13C-edited NOESYIso_waterisotropicsample_conditions_1
2D 1H-15N TROSYAniso_wateranisotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis, processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

ProcheckNMR, Laskowski and MacArthur - data analysis

xwinnmr, Bruker Biospin - collection

TOPSPIN, Bruker Biospin - collection

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking, processing

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB
GB AAB95314 EDM18826
REF NP_598209
SP O35820
AlphaFold O35820

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks