BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

BMRB Entry 16647

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/BMR16647
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry

Title: Solution NMR structure of SH3 domain from CPF_0587 (fragment 415-479) from Clostridium perfringens. Northeast Structural Genomics Consortium (NESG) Target CpR74A.

Deposition date: 2009-12-22 Original release date: 2010-01-06

Authors: Ramelot, Theresa; Cort, John; Maglaqui, Melissa; Ciccosanti, Colleen; Janjua, Haleema; Nair, R; Rost, Burkhard; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael

Citation: Ramelot, Theresa; Cort, John; Maglaqui, Melissa; Ciccosanti, Colleen; Janjua, Haleema; Nair, R; Rost, Burkhard; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano; Kennedy, Michael. "Solution NMR structure of SH3 domain from CPF_0587 (fragment 415-479) from Clostridium perfringens. Northeast Structural Genomics Consortium (NESG) Target CpR74A."  . ., .-..

Assembly members:
CPF_0587-SH3, polymer, 74 residues, 8300 Da.

Natural source:   Common Name: Clostridium perfringens   Taxonomy ID: 1502   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Clostridium perfringens

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

Entity Sequences (FASTA):
CPF_0587-SH3: MQGVVKVNSALNMRSGPGSN YGVIGTLRNNDKVEIIKEVD GWYEIRFNGKVGYASKSYIT IVNEGSLEHHHHHH

Data sets:
Data typeCount
13C chemical shifts307
15N chemical shifts76
1H chemical shifts482

Time Domain Data

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1CPF_0587-SH31

Entities:

Entity 1, CPF_0587-SH3 74 residues - 8300 Da.

1 non-native residue at the C-term (M). 8 non-native residues at C-terminus (LEHHHHHH)

1   METGLNGLYVALVALLYSVALASNSERALA
2   LEUASNMETARGSERGLYPROGLYSERASN
3   TYRGLYVALILEGLYTHRLEUARGASNASN
4   ASPLYSVALGLUILEILELYSGLUVALASP
5   GLYTRPTYRGLUILEARGPHEASNGLYLYS
6   VALGLYTYRALASERLYSSERTYRILETHR
7   ILEVALASNGLUGLYSERLEUGLUHISHIS
8   HISHISHISHIS

Samples:

NC_sample: MES 20 ± 1 mM; sodium chloride 100 ± 10 mM; calcium chloride 5 ± .25 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± .001 %; protein, [U-100% 13C; U-100% 15N], 0.8 ± .05 mM

NC_sample_in_D2O: MES 20 ± 1 mM; sodium chloride 100 ± 10 mM; calcium chloride 5 ± .25 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± .001 %; protein, [U-100% 13C; U-100% 15N], 0.8 ± .05 mM

NC5: MES 20 ± 1 mM; sodium chloride 100 ± 10 mM; calcium chloride 5 ± .25 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± .001 %; protein, [U-5% 13C; U-100% 15N], 0.9 ± .05 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQCNC_sampleisotropicsample_conditions_1
3D 1H-15N NOESYNC_sampleisotropicsample_conditions_1
3D 1H-13C NOESY aliphNC_sampleisotropicsample_conditions_1
3D HNCONC_sampleisotropicsample_conditions_1
3D HN(CO)CANC_sampleisotropicsample_conditions_1
3D CBCA(CO)NHNC_sampleisotropicsample_conditions_1
3D HNCACBNC_sampleisotropicsample_conditions_1
3D HBHA(CO)NHNC_sampleisotropicsample_conditions_1
3D HCCH-TOCSYNC_sampleisotropicsample_conditions_1
3D HCCH-COSYNC_sampleisotropicsample_conditions_1
3D (H)CCH-TOCSYNC_sample_in_D2Oisotropicsample_conditions_1
4D HCCH NOESYNC_sample_in_D2Oisotropicsample_conditions_1
3D 1H-13C NOESY aromNC_sampleisotropicsample_conditions_1
2D 1H-15N HSQC swNNC_sampleisotropicsample_conditions_1
2D 1H-15N HSQC NH2 onlyNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQC aromaticNC_sampleisotropicsample_conditions_1
T1 1D arrayNC_sampleisotropicsample_conditions_1
T1 rho 1D arrayNC_sampleisotropicsample_conditions_1
3D (H)CCONHNC_sampleisotropicsample_conditions_1
3D CCONHNC_sampleisotropicsample_conditions_1
2D 1H-13C HSQC in D2ONC_sample_in_D2Oisotropicsample_conditions_1
2D 1H-13C HSQC long ctNC5isotropicsample_conditions_1

Software:

NMRPipe v2008, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMR v6.1C, Varian - collection

TOPSPIN v2.1.4, Bruker Biospin - collection

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

X-PLOR NIH v2.20, Schwieters, Kuszewski, Tjandra and Clore - structure solution

SPARKY v3.113, Goddard - data analysis

PSVS v1.3, Bhattacharya and Montelione - structure validation

AutoAssign v2.3.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

PDBStat v5.0, (PDBStat) R. Tejero, G.T. Montelione - data analysis

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker AvanceIII 850 MHz

Related Database Links:

PDB

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