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Biological Magnetic Resonance Data Bank


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BMRB Entry 17246

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17246
MolProbity Validation Chart

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Title: Solution structure of the Streptococcus pneumoniae RrgB pilus backbone D1 domain   PubMed: 21367860

Deposition date: 2010-10-11 Original release date: 2011-03-30

Authors: Gentile, Maria Antonietta; Melchiorre, Sara; Emolo, Carla; Moschioni, Monica; Gianfaldoni, Claudia; Pancotto, Laura; Ferlenghi, Ilaria; Scarselli, Maria; Pansegrau, Werner; Veggi, Daniele; Merola, Marcello; Cantini, Francesca; Ruggiero, Paolo; Banci, Lucia; Masignani, Vega

Citation: Gentile, Maria Antonietta; Melchiorre, Sara; Emolo, Carla; Moschioni, Monica; Gianfaldoni, Claudia; Pancotto, Laura; Ferlenghi, Ilaria; Scarselli, Maria; Pansegrau, Werner; Veggi, Daniele; Merola, Marcello; Cantini, Francesca; Ruggiero, Paolo; Banci, Lucia; Masignani, Vega. "Structural and Functional Characterization of the Streptococcus pneumoniae RrgB Pilus Backbone D1 Domain."  J. Biol. Chem. 286, 14588-14597 (2011).

Assembly members:
DOMAIN_OF_A_CELL_WALL_SURFACE_ANCHOR_FAMILY_PROTEIN, polymer, 181 residues, 18545.027 Da.

Natural source:   Common Name: Streptococcus pneumoniae   Taxonomy ID: 1313   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Streptococcus pneumoniae

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

Entity Sequences (FASTA):
DOMAIN_OF_A_CELL_WALL_SURFACE_ANCHOR_FAMILY_PROTEIN: METASAATVFAAGTTTTSVT VHKLLATDGDMDKIANELET GNYAGNKVGVLPANAKEIAG VMFVWTNTNNEIIDENGQTL GVNIDPQTFKLSGAMPATAM KKLTEAEGAKFNTANLPAAK YKIYEIHSLSTYVGEDGATL TGSKAVPIEIELPLNDVVDA HVYPKNTEAKPKILEHHHHH H

Data sets:
Data typeCount
13C chemical shifts660
15N chemical shifts172
1H chemical shifts1168
heteronuclear NOE values150
order parameters150
T1 relaxation values150
T2 relaxation values150

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1CELL_WALL_SURFACE_ANCHOR1

Entities:

Entity 1, CELL_WALL_SURFACE_ANCHOR 181 residues - 18545.027 Da.

The C-terminal His-tag is removed from the pdb

1   METGLUTHRALASERALAALATHRVALPHE
2   ALAALAGLYTHRTHRTHRTHRSERVALTHR
3   VALHISLYSLEULEUALATHRASPGLYASP
4   METASPLYSILEALAASNGLULEUGLUTHR
5   GLYASNTYRALAGLYASNLYSVALGLYVAL
6   LEUPROALAASNALALYSGLUILEALAGLY
7   VALMETPHEVALTRPTHRASNTHRASNASN
8   GLUILEILEASPGLUASNGLYGLNTHRLEU
9   GLYVALASNILEASPPROGLNTHRPHELYS
10   LEUSERGLYALAMETPROALATHRALAMET
11   LYSLYSLEUTHRGLUALAGLUGLYALALYS
12   PHEASNTHRALAASNLEUPROALAALALYS
13   TYRLYSILETYRGLUILEHISSERLEUSER
14   THRTYRVALGLYGLUASPGLYALATHRLEU
15   THRGLYSERLYSALAVALPROILEGLUILE
16   GLULEUPROLEUASNASPVALVALASPALA
17   HISVALTYRPROLYSASNTHRGLUALALYS
18   PROLYSILELEUGLUHISHISHISHISHIS
19   HIS

Samples:

sample_1: CELL_WALL_SURFACE_ANCHOR, [U-95% 15N], 0.5 mM; H2O 90%; D2O 10%; phosphate buffer 20 mM

sample_2: CELL_WALL_SURFACE_ANCHOR 0.9 mM; H2O 90%; D2O 10%; phosphate buffer 20 mM

sample_3: CELL_WALL_SURFACE_ANCHOR, [U-95% 13C; U-95% 15N], 0.4 mM; H2O 90%; D2O 10%; phosphate buffer 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HN(COCA)CBsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HNCOCAsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HNCACOsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structural calculation

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - energy minimization

TOPSPIN v2.0, Bruker Biospin - processing

CARA v2.0, Keller and Wuthrich - spectra visualization

XEASY, Bartels et al. - spectra visualization

CING, (CING) Geerten W. Vuister , Jurgen F. Doreleijers and Alan Wilter Sousa da Silva - structure validation

Molmol, Koradi, Billeter and Wuthrich - structure visualization

TALOS, Cornilescu, Delaglio and Bax - Dihedral angle calculation

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB
EMBL CEO70617 CEV45859 CEV80893 CEV87170 CEV93515
GB AAK74623 ABS82086 ABS82156 ACO23362 ADI68988
REF WP_000836216 WP_000836217 WP_000836218 WP_000836219 WP_000836220

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts