BMRB Entry 25859
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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/BMR25859
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Title: Productive complex between MMP-12 and synthetic triple-helical collagen, revealed through paramagnetic NMR PubMed: 16855860
Deposition date: 2015-10-24 Original release date: 2016-02-22
Authors: Prior, Stephen; VanDoren, Steven
Citation: Bhaskaran, Rajagopalan; VanDoren, Steven. "1H, 13C, and 15N peak assignments and secondary structure of human macrophage metalloelastase (MMP-12) in its inhibitor-free state" J. Biomol. NMR 36, 55-55 (2006).
Assembly members:
MMP-12, polymer, 164 residues, 18235.561 Da.
THP, polymer, 36 residues, 3291.483 Da.
entity_ZN, non-polymer, 65.409 Da.
entity_CA, non-polymer, 40.078 Da.
entity_HOH, water, 18.015 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):
MMP-12: FREMPGGPVWRKHYITYRIN
NYTPDMNREDVDYAIRKAFQ
VWSNVTPLKFSKINTGMADI
LVVFARGAHGDFHAFDGKGG
ILAHAFGPGSGIGGDAHFDE
DEFWTTHSGGTNLFLTAVHE
IGHSLGLGHSSDPKAVMFPT
YKYVDINTFRLSADDIRGIQ
SLYG
THP: GPXGPXGPXGPXGPPGVVGE
QGEQGPXGPXGPXGPX
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 635 |
| 15N chemical shifts | 165 |
| 1H chemical shifts | 953 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | MMP-12 | 1 |
| 2 | THP_1 | 2 |
| 3 | THP_2 | 2 |
| 4 | THP_3 | 2 |
| 5 | ZINC ION_1 | 3 |
| 6 | ZINC ION_2 | 3 |
| 7 | CALCIUM ION_1 | 4 |
| 8 | CALCIUM ION_2 | 4 |
| 9 | CALCIUM ION_3 | 4 |
| 10 | water | 5 |
Entities:
Entity 1, MMP-12 164 residues - 18235.561 Da.
| 1 | PHE | ARG | GLU | MET | PRO | GLY | GLY | PRO | VAL | TRP | ||||
| 2 | ARG | LYS | HIS | TYR | ILE | THR | TYR | ARG | ILE | ASN | ||||
| 3 | ASN | TYR | THR | PRO | ASP | MET | ASN | ARG | GLU | ASP | ||||
| 4 | VAL | ASP | TYR | ALA | ILE | ARG | LYS | ALA | PHE | GLN | ||||
| 5 | VAL | TRP | SER | ASN | VAL | THR | PRO | LEU | LYS | PHE | ||||
| 6 | SER | LYS | ILE | ASN | THR | GLY | MET | ALA | ASP | ILE | ||||
| 7 | LEU | VAL | VAL | PHE | ALA | ARG | GLY | ALA | HIS | GLY | ||||
| 8 | ASP | PHE | HIS | ALA | PHE | ASP | GLY | LYS | GLY | GLY | ||||
| 9 | ILE | LEU | ALA | HIS | ALA | PHE | GLY | PRO | GLY | SER | ||||
| 10 | GLY | ILE | GLY | GLY | ASP | ALA | HIS | PHE | ASP | GLU | ||||
| 11 | ASP | GLU | PHE | TRP | THR | THR | HIS | SER | GLY | GLY | ||||
| 12 | THR | ASN | LEU | PHE | LEU | THR | ALA | VAL | HIS | GLU | ||||
| 13 | ILE | GLY | HIS | SER | LEU | GLY | LEU | GLY | HIS | SER | ||||
| 14 | SER | ASP | PRO | LYS | ALA | VAL | MET | PHE | PRO | THR | ||||
| 15 | TYR | LYS | TYR | VAL | ASP | ILE | ASN | THR | PHE | ARG | ||||
| 16 | LEU | SER | ALA | ASP | ASP | ILE | ARG | GLY | ILE | GLN | ||||
| 17 | SER | LEU | TYR | GLY |
Entity 2, THP_1 36 residues - 3291.483 Da.
| 1 | GLY | PRO | HYP | GLY | PRO | HYP | GLY | PRO | HYP | GLY | ||||
| 2 | PRO | HYP | GLY | PRO | PRO | GLY | VAL | VAL | GLY | GLU | ||||
| 3 | GLN | GLY | GLU | GLN | GLY | PRO | HYP | GLY | PRO | HYP | ||||
| 4 | GLY | PRO | HYP | GLY | PRO | HYP |
Entity 3, ZINC ION_1 - Zn - 65.409 Da.
| 1 | ZN |
Entity 4, CALCIUM ION_1 - Ca - 40.078 Da.
| 1 | CA |
Entity 5, water - 18.015 Da.
| 1 | HOH |
Samples:
Unprimed: MMP-12, [U-99% 15N], 0.4 mM; THP, TOAC labelled in P5 position, 0.6 mM
Primed: MMP-12, [U-100% 12C; U-100% 15N; U-100% 2H; U-100% 13CH3], 0.25 mM; THP, TOAC labelled in P8' position, 0.38 mM
sample_conditions_Unprimed: pH: 6.6; temperature: 299 K
sample_conditions_Primed: pH: 6.6; temperature: 299 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | Unprimed | isotropic | sample_conditions_Unprimed |
| 2D 1H-15N HSQC | Primed | isotropic | sample_conditions_Primed |
| 2D 1H-13C HSQC | Primed | isotropic | sample_conditions_Primed |
Software:
TOPSPIN, Bruker Biospin - collection, processing
Analysis, CCPN - chemical shift assignment, peak picking
HADDOCK v2.1, Alexandre Bonvin - structure solution
q_test.py, Stephen H. Prior - structure solution
GROMOS, van Gunsteren and Berendsen - refinement
NMR spectrometers:
- Bruker Avance 800 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts