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Biological Magnetic Resonance Data Bank


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BMRB Entry 18469

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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/BMR18469
MolProbity Validation Chart

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Title: Solution NMR Structure of apo YdbC from Lactococcus lactis, Northeast Structural Genomics Consortium (NESG) Target KR150

Deposition date: 2012-05-16 Original release date: 2012-06-04

Authors: Rossi, Paolo; Barbieri, Christopher; Aramini, James; Bini, Elisabetta; Lee, Hsiau-Wei; Janjua, Haleema; Ciccosanti, Colleen; Wang, Huang; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano

Citation: Rossi, Paolo; Barbieri, Christopher; Aramini, James; Bini, Elisabetta; Acton, Thomas; Xiao, Rong; Montelione, Gaetano. "Solution NMR Structure of apo YdbC from Lactococcus lactis, Northeast Structural Genomics Consortium (NESG) Target KR150"  To be published ., .-..

Assembly members:
KR150, polymer, 80 residues, 9488.850 Da.

Natural source:   Common Name: Lactococcus lactis   Taxonomy ID: 1358   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Lactococcus lactis

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

Entity Sequences (FASTA):
KR150: MADKLKFEIIEELIVLSENA KGWRKELNRVSWNDAEPKYD IRTWSPDHEKMGKGITLSEE EFGVLLKELGNKLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts338
15N chemical shifts77
1H chemical shifts538

Time Domain Data

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1KR150_11
2KR150_21

Entities:

Entity 1, KR150_1 80 residues - 9488.850 Da.

1   METALAASPLYSLEULYSPHEGLUILEILE
2   GLUGLULEUILEVALLEUSERGLUASNALA
3   LYSGLYTRPARGLYSGLULEUASNARGVAL
4   SERTRPASNASPALAGLUPROLYSTYRASP
5   ILEARGTHRTRPSERPROASPHISGLULYS
6   METGLYLYSGLYILETHRLEUSERGLUGLU
7   GLUPHEGLYVALLEULEULYSGLULEUGLY
8   ASNLYSLEUGLUHISHISHISHISHISHIS

Samples:

sample_1: KR150.020, [U-100% 13C; U-100% 15N], 1.1 mM; NaN3 0.02%; DTT 10 mM; NaCL 100 mM; D2O 10%; DSS 50 uM; TRIS-HCl 10 mM

sample_3: KR150.020, [U-5% 13C; U-100% 15N], 0.697 mM; NaN3 0.02%; DTT 10 mM; NaCL 100 mM; D2O 10%; DSS 50 uM; TRIS-HCl 10 mM

sample_2: KR150.019 1.2 mM; NaN3 0.02%; DTT 10 mM; NaCL 100 mM; D2O 10%; DSS 50 uM; TRIS-HCl 10 mM

sample_conditions_1: pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-13C arom NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D-X-filt-13C-editedNOESYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
1H-15N Hetnoesample_3isotropicsample_conditions_1
1D T1sample_1isotropicsample_conditions_1
1D T2(cpmg)sample_1isotropicsample_conditions_1
j-mod HSQC (rdc)sample_3anisotropicsample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinemen,structure solution,geometry optimization

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

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

TOPSPIN, Bruker Biospin - collection

VNMRJ, Varian - collection

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

SPARKY, Goddard - data analysis

TALOS+, Shen, Cornilescu, Delaglio and Bax - geometry optimization

PALES, PALES (Zweckstetter, Bax) - geometry optimization

PSVS, Bhattacharya, Montelione - structure validation

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Varian INOVA 600 MHz

Related Database Links:

BMRB 18496
PDB
DBJ BAL50274 GAM81529
EMBL CAL96933 CDG04366 CDI47747
GB AAK04411 ABJ71956 ADA64134 ADJ59348 ADZ62963
REF NP_266469 WP_003131683 WP_012897170 WP_015425778 WP_046124177

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