BMRB Entry 34666

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34666
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Title:
NMR Structure of RgpB C-terminal Domain
Deposition date:
2021-09-16
Original release date:
2022-09-21
Authors:
Dorgan, B.; Curtis, M.; Garnett, J.
Citation:

Citation: Dorgan, B.; Curtis, M.; Garnett, J.. "NMR structure of RgpB C-terminal Domain"  To be published ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 90 residues, 9854.143 Da.

Natural source:

Natural source:   Common Name: Porphyromonas gingivalis   Taxonomy ID: 837   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Porphyromonas gingivalis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pET46

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MAHHHHHHVDDDDKMGTSIA DVANDKPYTVAVSGKTITVE SPAAGLTIFDMNGRRVATAK NRMVFEAQNGVYAVRIATEG KTYTEKVIVK

Data sets:
Data typeCount
13C chemical shifts353
15N chemical shifts83
1H chemical shifts541

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 90 residues - 9854.143 Da.

1   METALAHISHISHISHISHISHISVALASP
2   ASPASPASPLYSMETGLYTHRSERILEALA
3   ASPVALALAASNASPLYSPROTYRTHRVAL
4   ALAVALSERGLYLYSTHRILETHRVALGLU
5   SERPROALAALAGLYLEUTHRILEPHEASP
6   METASNGLYARGARGVALALATHRALALYS
7   ASNARGMETVALPHEGLUALAGLNASNGLY
8   VALTYRALAVALARGILEALATHRGLUGLY
9   LYSTHRTYRTHRGLULYSVALILEVALLYS

Samples:

sample_1: RgpB-CTD (G662-K736), [U-13C; U-15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 2 mM

sample_conditions_1: ionic strength: 70 mM; pH: 6; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
HBCBCGCDHDsample_1isotropicsample_conditions_1
HBCBCGCDCEHEsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

ARIA v2.3, Linge, O'Donoghue and Nilges - structure calculation

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

DANGLE v1.1.1, Cheung, Maguire, Stevens and Broadhurst - geometry optimization

WHAT IF, Vriend - data analysis

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

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

NMR spectrometers:

  • Bruker AVANCE III HD 900 MHz

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