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Biological Magnetic Resonance Data Bank


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BMRB Entry 15683

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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/BMR15683
MolProbity Validation Chart

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Title: Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli, Northeast Structural Genomics Consortium Target ER553.

Deposition date: 2008-03-14 Original release date: 2008-03-19

Authors: Ramelot, Theresa; Zhao, Li; Hamilton, Kieth; Maglaqui, Melissa; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael

Citation: Ramelot, Theresa; Zhao, Li; Hamilton, Kieth; Maglaqui, Melissa; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael. "Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli. Northeast Structural Genomics Consortium Target ER553."  . ., .-..

Assembly members:
YiaD, polymer, 149 residues, 16056.109 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Escherichia coli

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

Entity Sequences (FASTA):
YiaD: YYMDVQEAKLRDKMRGTGVS VTRSGDNIILNMPNNVTFDS SSATLKPAGANTLTGVAMVL KEYPKTAVNVIGYTDSTGGH DLNMRLSQQRADSVASALIT QGVDASRIRTQGLGPANPIA SNSTAEGKAQNRRVEITLSP LLEHHHHHH

Data typeCount
13C chemical shifts596
15N chemical shifts161
1H chemical shifts998

Time Domain Data

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1YiaD1

Entities:

Entity 1, YiaD 149 residues - 16056.109 Da.

C-terminal residues 59-199 of YiaD followed by 8 non-native C-terminal residues (LEHHHH)

1   TYRTYRMETASPVALGLNGLUALALYSLEU
2   ARGASPLYSMETARGGLYTHRGLYVALSER
3   VALTHRARGSERGLYASPASNILEILELEU
4   ASNMETPROASNASNVALTHRPHEASPSER
5   SERSERALATHRLEULYSPROALAGLYALA
6   ASNTHRLEUTHRGLYVALALAMETVALLEU
7   LYSGLUTYRPROLYSTHRALAVALASNVAL
8   ILEGLYTYRTHRASPSERTHRGLYGLYHIS
9   ASPLEUASNMETARGLEUSERGLNGLNARG
10   ALAASPSERVALALASERALALEUILETHR
11   GLNGLYVALASPALASERARGILEARGTHR
12   GLNGLYLEUGLYPROALAASNPROILEALA
13   SERASNSERTHRALAGLUGLYLYSALAGLN
14   ASNARGARGVALGLUILETHRLEUSERPRO
15   LEULEUGLUHISHISHISHISHISHIS

Samples:

NC_sample: entity, [U-100% 13C; U-100% 15N], 1.9 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %

NC5_sample: entity, [U-5% 13C; U-100% 15N], 1.3 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %

NC_sample_in_D2O: entity, [U-100% 13C; U-100% 15N], 1.9 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQC (arom ct)NC_sampleisotropicsample_conditions_1
2D 1H-13C HSQCNC5_sampleisotropicsample_conditions_1
3D 1H-15N NOESYNC_sampleisotropicsample_conditions_1
3D 1H-13C NOESYNC_sampleisotropicsample_conditions_1
3D 1H-13C NOESYNC_sample_in_D2Oisotropicsample_conditions_1
3D HNCONC_sampleisotropicsample_conditions_1
3D HNCANC_sampleisotropicsample_conditions_1
3D HN(CO)CANC_sampleisotropicsample_conditions_1
3D HNCACBNC_sampleisotropicsample_conditions_1
3D CBCA(CO)NHNC_sampleisotropicsample_conditions_1
3D C(CO)NHNC_sampleisotropicsample_conditions_1
3D HBHA(CO)NHNC_sampleisotropicsample_conditions_1
3D H(CCO)NHNC_sampleisotropicsample_conditions_1
3D HCCH-TOCSYNC_sampleisotropicsample_conditions_1
3D HCCH-COSYNC_sampleisotropicsample_conditions_1
4D CC NOESYNC_sample_in_D2Oisotropicsample_conditions_1
2D 1H-13C HSQC (arom no ct)NC_sampleisotropicsample_conditions_1

Software:

NMRPipe vlinux9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMR v6.1C, Varian - collection

TOPSPIN v2.1, Bruker Biospin - collection

AutoStruct v2.1.1, Huang, Tejero, Powers and Montelione - data analysis

X-PLOR NIH v2.15.0, Schwieters, Kuszewski, Tjandra and Clore - structure solution

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

SPARKY v3.113, Goddard - data analysis

PSVS v1.3, Bhattacharya and Montelione - structure solution

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker AvanceIII 850 MHz

Related Database Links:

PDB
DBJ BAB37860 BAE77743 BAG79349 BAI28203 BAI33377
EMBL CAP78012 CAQ33870 CAR00514 CAR05180 CAR10226
GB AAB18529 AAG58701 AAN45037 AAN82806 AAP19151
REF NP_312464 NP_709330 WP_000470321 WP_000495106 WP_000747546
SP P37665

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