BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 16096

Title: SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME CHAPERONE CCME FROM DESULFOVIBRIO VULGARIS. NORTHEAST STRUCTURAL GENOMICS TARGET DVR115G.

Authors: Aramini, James; Rossi, Paolo; Lee, Hsiau-Wei; Alexander, Lemak; Wang, Huang; Foote, Erica; Jiang, Mei; Xiao, Rong; Nair, Rajesh; Swapna, G.; Acton, Thomas; Rost, Burkhard; Everett, John; Montelione, Gaetano

Citation: Aramini, James; Rossi, Paolo; Lee, Hsiau-Wei; Alexander, Lemak; Wang, Huang; Foote, Erica; Jiang, Mei; Xiao, Rong; Nair, Rajesh; Swapna, G.; Acton, Thomas; Rost, Burkhard; Everett, John; Montelione, Gaetano. "SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME CHAPERONE CCME FROM DESULFOVIBRIO VULGARIS. NORTHEAST STRUCTURAL GENOMICS TARGET DVR115G."  Not known ., .-..

Assembly members:
DvR115G, polymer, 94 residues, 10375.994 Da.

Natural source:   Common Name: Desulfovibrio vulgaris   Taxonomy ID: 881   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Desulfovibrio vulgaris

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

Entity Sequences (FASTA):
DvR115G: MATPQDKLHTVRLFGTVAAD GLTMLDGAPGVRFRLEDKDN TSKTVWVLYKGAVPDTFKPG VEVIIEGGLAPGEDTFKART LMTKCPLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts392
15N chemical shifts87
1H chemical shifts618
residual dipolar couplings49

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DvR115G1

Entities:

Entity 1, DvR115G 94 residues - 10375.994 Da.

The N-terminal Met and C-terminal affinity tag (LEHHHHHH) are cloning artefacts.

1   METALATHRPROGLNASPLYSLEUHISTHR
2   VALARGLEUPHEGLYTHRVALALAALAASP
3   GLYLEUTHRMETLEUASPGLYALAPROGLY
4   VALARGPHEARGLEUGLUASPLYSASPASN
5   THRSERLYSTHRVALTRPVALLEUTYRLYS
6   GLYALAVALPROASPTHRPHELYSPROGLY
7   VALGLUVALILEILEGLUGLYGLYLEUALA
8   PROGLYGLUASPTHRPHELYSALAARGTHR
9   LEUMETTHRLYSCYSPROLEUGLUHISHIS
10   HISHISHISHIS

Samples:

sample_1: DvR115G, [U-100% 13C; U-100% 15N], 1.3 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM

sample_2: DvR115G, [U-5% 13C; U-100% 15N], 0.56 mM; ammonium acetate 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM

sample_3: DvR115G, [U-5% 13C; U-100% 15N], 70 %v/v; PEG/hexanol 4.2%

sample_conditions_1: ionic strength: 0.2 M; pH: 4.5; pressure: 1.0 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D simultaneous CN NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC high res. (L/V methyl stereoassignment)sample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D C(CO)NH TOCSYsample_1isotropicsample_conditions_1
3D HCCH-COSY aliphaticsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D (H)CCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
2D 1H-15N hetNOEsample_1isotropicsample_conditions_1
1D 1H-15N T1 and T2sample_1isotropicsample_conditions_1
2D 1H-15N TROSY (for N-H RDCs)sample_3anisotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, N15 T1/T2 data analysis

VNMRJ v2.1B, Varian - collection

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.112, Goddard - data analysis, peak picking

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

AutoAssign v2.4.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment, validation

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

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

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - RPF analysis

PSVS v1.3, Bhattacharya and Montelione - structure quality analysis

PDBStat v5.1, Tejero and Montelione - PDB coordinate analysis

PALES, Zweckstetter and Bax - Prediction of molecular alignment

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Varian INOVA 600 MHz
  • Bruker Avance 600 MHz

Related Database Links:

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