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BMRB Entry 15734

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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/BMR15734
MolProbity Validation Chart

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Title: Solution Structure of cGMP-binding GAF domain of Phosphodiesterase 5   PubMed: 18534985

Deposition date: 2008-04-16 Original release date: 2008-08-28

Authors: Heikaus, Clemens; Stout, Joseph; Sekharan, Monica; Eakin, Catherine; Rajagopal, Ponni; Brzovic, Peter; Beavo, Joseph; Klevit, Rachel

Citation: Heikaus, Clemens; Stout, Joseph; Sekharan, Monica; Eakin, Catherine; Rajagopal, Ponni; Brzovic, Peter; Beavo, Joseph; Klevit, Rachel. "Solution Structure of the cGMP Binding GAF Domain from Phosphodiesterase 5: INSIGHTS INTO NUCLEOTIDE SPECIFICITY, DIMERIZATION, AND cGMP-DEPENDENT CONFORMATIONAL CHANGE"  J. Biol. Chem. 283, 22749-22759 (2008).

Assembly members:
mPDE5_GAFA, polymer, 176 residues, 20037.4 Da.
GUANOSINE-3',5'-MONOPHOSPHATE, non-polymer, 345.205 Da.

Natural source:   Common Name: Mus musculus   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

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

Entity Sequences (FASTA):
mPDE5_GAFA: MDVTALCHKIFLHIHGLISA DRYSLFLVCEDSSKDKFLIS RLFDVAEGSTLEEASNNCIR LEWNKGIVGHVAAFGEPLNI KDAYEDPRFNAEVDQITGYK TQSILCMPIKNHREEVVGVA QAINKKSGNGGTFTEKDEKD FAEYLAFCGEVLHNAQLYET SLLENKRNLEHHHHHH

Data sets:
Data typeCount
1H chemical shifts978
13C chemical shifts636
15N chemical shifts151

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2GUANOSINE-3',5'-MONOPHOSPHATE2

Entities:

Entity 1, entity_1 176 residues - 20037.4 Da.

1   METASPVALTHRALALEUCYSHISLYSILE
2   PHELEUHISILEHISGLYLEUILESERALA
3   ASPARGTYRSERLEUPHELEUVALCYSGLU
4   ASPSERSERLYSASPLYSPHELEUILESER
5   ARGLEUPHEASPVALALAGLUGLYSERTHR
6   LEUGLUGLUALASERASNASNCYSILEARG
7   LEUGLUTRPASNLYSGLYILEVALGLYHIS
8   VALALAALAPHEGLYGLUPROLEUASNILE
9   LYSASPALATYRGLUASPPROARGPHEASN
10   ALAGLUVALASPGLNILETHRGLYTYRLYS
11   THRGLNSERILELEUCYSMETPROILELYS
12   ASNHISARGGLUGLUVALVALGLYVALALA
13   GLNALAILEASNLYSLYSSERGLYASNGLY
14   GLYTHRPHETHRGLULYSASPGLULYSASP
15   PHEALAGLUTYRLEUALAPHECYSGLYGLU
16   VALLEUHISASNALAGLNLEUTYRGLUTHR
17   SERLEULEUGLUASNLYSARGASNLEUGLU
18   HISHISHISHISHISHIS

Entity 2, GUANOSINE-3',5'-MONOPHOSPHATE - C10 H12 N5 O7 P - 345.205 Da.

1   35G

Samples:

unlabeled_5A: GUANOSINE-3',5'-MONOPHOSPHATE0.5 – 1.2 mM; mPDE5_GAFA0.5 – 1.2 mM; sodium chloride 150 mM; PMSF 1 mM; DTT 1-5 mM; EDTA 0.1 mM; sodium phosphate 25 mM; D2O 10%; H2O 90%

15N_5A: GUANOSINE-3',5'-MONOPHOSPHATE0.5 – 1.2 mM; mPDE5_GAFA, [U-100% 15N], 0.5 – 1.2 mM; sodium chloride 150 mM; PMSF 1 mM; DTT 1-5 mM; EDTA 0.1 mM; sodium phosphate 25 mM; D2O 10%; H2O 90%

2H_13C_15N_5A: GUANOSINE-3',5'-MONOPHOSPHATE0.5 – 1.2 mM; mPDE5_GAFA, [U-100% 13C; U-100% 15N; 80% 2H], 0.5 – 1.2 mM; sodium chloride 150 mM; PMSF 1 mM; DTT 1-5 mM; EDTA 0.1 mM; sodium phosphate 25 mM; D2O 10%; H2O 90%

13C_15N_5A: GUANOSINE-3',5'-MONOPHOSPHATE0.5 – 1.2 mM; mPDE5_GAFA, [U-100% 13C; U-100% 15N], 0.5 – 1.2 mM; sodium chloride 150 mM; PMSF 1 mM; DTT 1-5 mM; EDTA 0.1 mM; sodium phosphate 25 mM; D2O 10%; H2O 90%

15N_5A_2: GUANOSINE-3',5'-MONOPHOSPHATE0.5 – 1.2 mM; mPDE5_GAFA, [U-100% 15N], 0.5 – 1.2 mM; sodium chloride 150 mM; PMSF 1 mM; DTT 1-5 mM; EDTA 0.1 mM; sodium phosphate 25 mM; D2O 100%

13C_15N_5A_2: GUANOSINE-3',5'-MONOPHOSPHATE0.5 – 1.2 mM; mPDE5_GAFA, [U-100% 13C; U-100% 15N], 0.5 – 1.2 mM; sodium chloride 150 mM; PMSF 1 mM; DTT 1-5 mM; EDTA 0.1 mM; sodium phosphate 25 mM; D2O 100%

sample_conditions_1: temperature: 310 K; pH: 7; pressure: 1 atm; ionic strength: 150 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15N_5Aisotropicsample_conditions_1
2D 1H-13C HSQC13C_15N_5Aisotropicsample_conditions_1
2D 1H-1H NOESYunlabeled_5Aisotropicsample_conditions_1
3D HNCO2H_13C_15N_5Aisotropicsample_conditions_1
3D HNCA2H_13C_15N_5Aisotropicsample_conditions_1
3D HNCACB2H_13C_15N_5Aisotropicsample_conditions_1
3D CBCA(CO)NH2H_13C_15N_5Aisotropicsample_conditions_1
3D HCCH-COSY13C_15N_5Aisotropicsample_conditions_1
3D HN(COCA)CB2H_13C_15N_5Aisotropicsample_conditions_1
3D HCCH-TOCSY13C_15N_5Aisotropicsample_conditions_1
3D 1H-15N NOESY13C_15N_5Aisotropicsample_conditions_1
3D 1H-13C NOESY13C_15N_5A_2isotropicsample_conditions_1
3D HN(CO)CA2H_13C_15N_5Aisotropicsample_conditions_1
2D 1H-15N HSQC15N_5A_2isotropicsample_conditions_1

Software:

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

CYANA v2.0, Guntert, Mumenthaler and Wuthrich - structure solution

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

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

ModelFree, Palmer - data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

  • Bruker DMX 500 MHz
  • Bruker DMX 600 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 800 MHz
  • Varian INOVA 900 MHz

Related Database Links:

PDB
DBJ BAA84660 BAC27332
GB EGW02508
TPG DAA28931

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