BMRB Entry 18978

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18978
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Solution structure of Ph1500: a homohexameric protein centered on a 12-bladed beta-propeller
Deposition date:
2013-01-28
Original release date:
2013-03-01
Authors:
Varnay, Ilka; Truffault, Vincent; Kessler, Horst; Coles, Murray
Citation:

Citation: Varnay, Ilka; Truffault, Vincent; Djuranovic, Sergej; Ursinus, Astrid; Coles, Murray; Kessler, Horst. "Optimized measurement temperature gives access to the solution structure of a 49 kDa homohexameric -propeller."  J. Am. Chem. Soc. 132, 15692-15698 (2010).
PubMed: 20961124

Assembly members:

Assembly members:
Ph1500, polymer, 147 residues, 16728.898 Da.
Ph1500N, polymer, 83 residues, 16728.898 Da.
Ph1500C, polymer, 78 residues, 16728.898 Da.

Natural source:

Natural source:   Common Name: Euryarchaeotes   Taxonomy ID: 53953   Superkingdom: Archaea   Kingdom: not available   Genus/species: Pyrococcus horikoshii

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET28b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ph1500: EGVIMSELKLKPLPKVELPP DFVDVIRIKLQGKTVRTGDV IGISILGKEVKFKVVQAYPS PLRVEDRTKITLVTHPVDVL EAKIKGIKDVILDENLIVVI TEENEVLIFNQNLEELYRGK FENLNKVLVRNDLVVIIDEQ KLTLIRT
Ph1500N: MHHHHHHEGVIMSELKLKPL PKVELPPDFVDVIRIKLQGK TVRTGDVIGISILGKEVKFK VVQAYPSPLRVEDRTKITLV THP
Ph1500C: MHHHHHHVDVLEAKIKGIKD VILDENLIVVITEENEVLIF NQNLEELYRGKFENLNKVLV RNDLVVIIDEQKLTLIRT

Data sets:
Data typeCount
13C chemical shifts674
15N chemical shifts131
1H chemical shifts1125

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Ph1500_11
2Ph1500_21
3Ph1500_31
4Ph1500_41
5Ph1500_51
6Ph1500_61
7Ph1500N2
8Ph1500C3

Entities:

Entity 1, Ph1500_1 147 residues - 16728.898 Da.

The first four residues are an artefact of an incorrectly annotated start methionine. Residue numbering refers to the correct start

1   GLUGLYVALILEMETSERGLULEULYSLEU
2   LYSPROLEUPROLYSVALGLULEUPROPRO
3   ASPPHEVALASPVALILEARGILELYSLEU
4   GLNGLYLYSTHRVALARGTHRGLYASPVAL
5   ILEGLYILESERILELEUGLYLYSGLUVAL
6   LYSPHELYSVALVALGLNALATYRPROSER
7   PROLEUARGVALGLUASPARGTHRLYSILE
8   THRLEUVALTHRHISPROVALASPVALLEU
9   GLUALALYSILELYSGLYILELYSASPVAL
10   ILELEUASPGLUASNLEUILEVALVALILE
11   THRGLUGLUASNGLUVALLEUILEPHEASN
12   GLNASNLEUGLUGLULEUTYRARGGLYLYS
13   PHEGLUASNLEUASNLYSVALLEUVALARG
14   ASNASPLEUVALVALILEILEASPGLUGLN
15   LYSLEUTHRLEUILEARGTHR

Entity 2, Ph1500N 83 residues - 16728.898 Da.

The first seven residues are a purification tag. The next four residues are an artefact of an incorrectly annotated start methionine.

1   METHISHISHISHISHISHISGLUGLYVAL
2   ILEMETSERGLULEULYSLEULYSPROLEU
3   PROLYSVALGLULEUPROPROASPPHEVAL
4   ASPVALILEARGILELYSLEUGLNGLYLYS
5   THRVALARGTHRGLYASPVALILEGLYILE
6   SERILELEUGLYLYSGLUVALLYSPHELYS
7   VALVALGLNALATYRPROSERPROLEUARG
8   VALGLUASPARGTHRLYSILETHRLEUVAL
9   THRHISPRO

Entity 3, Ph1500C 78 residues - 16728.898 Da.

The first seven residues are a purification tag

1   METHISHISHISHISHISHISVALASPVAL
2   LEUGLUALALYSILELYSGLYILELYSASP
3   VALILELEUASPGLUASNLEUILEVALVAL
4   ILETHRGLUGLUASNGLUVALLEUILEPHE
5   ASNGLNASNLEUGLUGLULEUTYRARGGLY
6   LYSPHEGLUASNLEUASNLYSVALLEUVAL
7   ARGASNASPLEUVALVALILEILEASPGLU
8   GLNLYSLEUTHRLEUILEARGTHR

Samples:

sample_1: Ph1500C, [U-100% 13C; U-100% 15N], 1.2 mM; sodium phosphate 20 mM; sodium chloride 250 mM; H2O 90%; D2O 10%

sample_2: Ph1500C, [U-85% 2H; U-100% 13C; U-100% 15N], 0.6 mM; sodium phosphate 20 mM; sodium chloride 250 mM; H2O 90%; D2O 10%

sample_3: Ph1500N, [U-100% 13C; U-100% 15N], 1.0 mM; sodium phosphate 50 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_4: Ph1500N, [U-100% 15N], 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_5: Ph1500, [U-85% 2H; U-100% 13C; U-100% 15N], 0.6 mM; sodium phosphate 20 mM; sodium chloride 250 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 300 K

sample_conditions_2: ionic strength: 250 mM; pH: 7.2; pressure: 1 atm; temperature: 353 K

sample_conditions_3: ionic strength: 250 mM; pH: 7.2; pressure: 1 atm; temperature: 318 K

Experiments:

NameSampleSample stateSample conditions
3D HNCOsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNHAsample_4isotropicsample_conditions_1
3D HNHBsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_4isotropicsample_conditions_1
3D NNH-NOESYsample_4isotropicsample_conditions_1
3D CNH-NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D CCH-NOESYsample_3isotropicsample_conditions_1
2D 15N-filtered 1H-1H NOESYsample_4isotropicsample_conditions_1
3D trHNCOsample_2isotropicsample_conditions_3
3D trHN(CA)COsample_2isotropicsample_conditions_3
3D trHNCAsample_2isotropicsample_conditions_3
3D trHNCACBsample_2isotropicsample_conditions_3
3D trHNCOsample_1isotropicsample_conditions_2
3D trHNCAsample_1isotropicsample_conditions_2
3D trHN(CA)COsample_1isotropicsample_conditions_2
3D HN(CA)HAsample_1isotropicsample_conditions_2
3D H(C)CH-TOCSYsample_1isotropicsample_conditions_2
3D (H)CCH-COSYsample_1isotropicsample_conditions_2
3D (H)CCH-COSYsample_1isotropicsample_conditions_2
2D 15N-filtered 1H-1H NOESYsample_3isotropicsample_conditions_2
3D 1H-15N NOESYsample_1isotropicsample_conditions_2
3D NNH-NOESYsample_1isotropicsample_conditions_2
3D CNH-NOESYsample_1isotropicsample_conditions_2
3D 1H-13C NOESYsample_1isotropicsample_conditions_2
3D CCH-NOESYsample_1isotropicsample_conditions_2
2D 1H-15N TROSYsample_5isotropicsample_conditions_2
2D 1H-15N CRINEPTsample_2isotropicsample_conditions_2
3D HCCH-TOCSYsample_3isotropicsample_conditions_1

Software:

xwinnmr v3.6, Bruker Biospin - collection, processing

SPARKY v3.110, Goddard - data analysis

X-PLOR NIH v2.2.1, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

  • Bruker DMX 600 MHz
  • Bruker DMX 750 MHz
  • Bruker DMX 900 MHz

Related Database Links:

UNP O59169 O59169
AlphaFold O59169 O59169 O59169

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