BMRB Entry 25564
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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/BMR25564
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Title: Structure of the Third Type III Domain from Human Fibronectin PubMed: 26517579
Deposition date: 2015-04-04 Original release date: 2015-11-09
Authors: Stine, Jessica; Sun, Yizhi; Armstrong, Geoffrey; Briknarova, Klara
Citation: Stine, Jessica; Sun, Yizhi; Armstrong, Geoffrey; Briknarova, Klara. "Structure and Unfolding of the Third Type III Domain from Human Fibronectin" Biochemistry 54, 6724-6733 (2015).
Assembly members:
entity, polymer, 106 residues, 11337.317 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: GSHMGTTTAPDAPPDPTVDQ
VDDTSIVVRWSRPQAPITGY
RIVYSPSVEGSSTELNLPET
ANSVTLSDLQPGVQYNITIY
AVEENQESTPVVIQQETTGT
PRSDGT
- assigned_chemical_shifts
Data type | Count |
13C chemical shifts | 439 |
15N chemical shifts | 99 |
1H chemical shifts | 681 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | entity | 1 |
Entities:
Entity 1, entity 106 residues - 11337.317 Da.
The recombinant protein contains six extraneous amino acids at the N-terminus, residues 808-905 of human fibronectin, and two extraneous amino acids at the C-terminus (gshmgtTTAP...PRSDgt).
1 | GLY | SER | HIS | MET | GLY | THR | THR | THR | ALA | PRO | ||||
2 | ASP | ALA | PRO | PRO | ASP | PRO | THR | VAL | ASP | GLN | ||||
3 | VAL | ASP | ASP | THR | SER | ILE | VAL | VAL | ARG | TRP | ||||
4 | SER | ARG | PRO | GLN | ALA | PRO | ILE | THR | GLY | TYR | ||||
5 | ARG | ILE | VAL | TYR | SER | PRO | SER | VAL | GLU | GLY | ||||
6 | SER | SER | THR | GLU | LEU | ASN | LEU | PRO | GLU | THR | ||||
7 | ALA | ASN | SER | VAL | THR | LEU | SER | ASP | LEU | GLN | ||||
8 | PRO | GLY | VAL | GLN | TYR | ASN | ILE | THR | ILE | TYR | ||||
9 | ALA | VAL | GLU | GLU | ASN | GLN | GLU | SER | THR | PRO | ||||
10 | VAL | VAL | ILE | GLN | GLN | GLU | THR | THR | GLY | THR | ||||
11 | PRO | ARG | SER | ASP | GLY | THR |
Samples:
sample_1: entity, [U-99% 13C; U-99% 15N], 0.6 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; H2O 90%; D2O 10%
sample_2: entity, [U-99% 15N], 0.6 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; H2O 90%; D2O 10%
sample_3: entity 0.6 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; H2O 90%; D2O 10%
sample_4: entity 0.6 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; D2O 100%
sample_5: entity, [U-99% 13C; U-99% 15N], 0.9 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; entity 0.9 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0.17 M; pH: 7.5; pressure: 1 atm; temperature: 298.15 K
Experiments:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
3D HNCO | sample_1 | isotropic | sample_conditions_1 |
3D HN(CA)CO | sample_1 | isotropic | sample_conditions_1 |
3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
3D CCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
2D HBCB(CGCD)HD | sample_1 | isotropic | sample_conditions_1 |
3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
2D 15N HMQC | sample_2 | isotropic | sample_conditions_1 |
2D DQF-COSY | sample_3 | isotropic | sample_conditions_1 |
2D 1H-1H TOCSY | sample_3 | isotropic | sample_conditions_1 |
2D 1H-1H NOESY | sample_3 | isotropic | sample_conditions_1 |
2D DQF-COSY | sample_4 | isotropic | sample_conditions_1 |
2D 1H-1H TOCSY | sample_4 | isotropic | sample_conditions_1 |
2D 1H-1H NOESY | sample_4 | isotropic | sample_conditions_1 |
2D 13C/15N-filtered 13C/15N-edited NOESY | sample_5 | isotropic | sample_conditions_1 |
Software:
VNMRJ, Agilent - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CcpNmr, CCPN - chemical shift assignment, data analysis, peak picking
ARIA, Linge, O'Donoghue and Nilges - refinement, structure solution
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution
TALOS, Cornilescu, Delaglio and Bax - generation of torsion angle restraints
NMR spectrometers:
- Varian Varian NMR System 600 MHz
- Varian Varian NMR System 800 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts