BMRB Entry 18943

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18943
MolProbity Validation Chart

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Title:
N-terminal domain of pneumococcal PhtD protein with bound Zn(II)
Deposition date:
2013-01-08
Original release date:
2013-11-18
Authors:
Bersch, Beate; Bougault, C.; Favier, A.; Gabel, F.; Roux, L.; Vernet, T.; Durmort, C.
Citation:

Citation: Bersch, Beate; Bougault, Catherine; Roux, Laure; Favier, Adrien; Vernet, Thierry; Durmort, Claire. "New insights into histidine triad proteins: solution structure of a Streptococcus pneumoniae PhtD domain and zinc transfer to AdcAII."  PLoS ONE 8, e81168-e81168 (2013).
PubMed: 24312273

Assembly members:

Assembly members:
PNEUMOCOCCAL_HISTIDINE_TRIAD_PROTEIN_D, polymer, 138 residues, 15756.3638 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pLIM09-t-phtD

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PNEUMOCOCCAL_HISTIDINE_TRIAD_PROTEIN_D: GGQVKKESNRVSYIDGDQAG QKAENLTPDEVSKREGINAE QIVIKITDQGYVTSHGDHYH YYNGKVPYDAIISEELLMKD PNYQLKDSDIVNEIKGGYVI KVDGKYYVYLKDAAHADNIR TKEEIKRQKQERSHNHNS

Data sets:
Data typeCount
13C chemical shifts529
15N chemical shifts128
1H chemical shifts816

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1PNEUMOCOCCAL HISTIDINE TRIAD PROTEIN D1
2ZINC ION2

Entities:

Entity 1, PNEUMOCOCCAL HISTIDINE TRIAD PROTEIN D 138 residues - 15756.3638 Da.

1   GLYGLYGLNVALLYSLYSGLUSERASNARG
2   VALSERTYRILEASPGLYASPGLNALAGLY
3   GLNLYSALAGLUASNLEUTHRPROASPGLU
4   VALSERLYSARGGLUGLYILEASNALAGLU
5   GLNILEVALILELYSILETHRASPGLNGLY
6   TYRVALTHRSERHISGLYASPHISTYRHIS
7   TYRTYRASNGLYLYSVALPROTYRASPALA
8   ILEILESERGLUGLULEULEUMETLYSASP
9   PROASNTYRGLNLEULYSASPSERASPILE
10   VALASNGLUILELYSGLYGLYTYRVALILE
11   LYSVALASPGLYLYSTYRTYRVALTYRLEU
12   LYSASPALAALAHISALAASPASNILEARG
13   THRLYSGLUGLUILELYSARGGLNLYSGLN
14   GLUARGSERHISASNHISASNSER

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: PNEUMOCOCCAL HISTIDINE TRIAD PROTEIN D, [U-13C; U-15N], 0.8 mM

sample_2: PNEUMOCOCCAL HISTIDINE TRIAD PROTEIN D 0.8 mM

sample_conditions_1_1: ionic strength: 0.0 mM; pH: 6.300; pressure: 1 atm; temperature: 308.000 K

sample_conditions_1_1_2: ionic strength: 50.000 mM; pH: 6.300; pressure: 1 atm; temperature: 308.000 K

Experiments:

NameSampleSample stateSample conditions
15N-HSQCsample_1solutionsample_conditions_1_1
13C-HSQCsample_1solutionsample_conditions_1_1
3D-15N-NOESYsample_1solutionsample_conditions_1_1
3D-13C-NOESYsample_1solutionsample_conditions_1_1
2D-NOESYsample_2solutionsample_conditions_1_1_2

Software:

AutoDep v4.3, PBBe - chemical shift assignment

CNS vany, Brunger - data analysis

CYANA vany, Guntert, Mumenthaler and Wuthrich - chemical shift assignment

NMR spectrometers:

  • Varian VNMRS800 800 MHz

Related Database Links:

UNP Q04KS8_STRP2
PDB
EMBL CAR68753 CBW34555 CBW36545 CEO61225 CEO63999
GB AAK06759 AAK06760 AAK75120 AAK75283 AAK99711
REF NP_358501 WP_000279427 WP_000279428 WP_000700283 WP_000700284
AlphaFold A0A0H2ZP82

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