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
MolProbity Validation Chart

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Title:
Productive complex between MMP-12 and synthetic triple-helical collagen, revealed through paramagnetic NMR
Deposition date:
2015-10-24
Original release date:
2016-02-22
Authors:
Prior, Stephen; VanDoren, Steven
Citation:

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).
PubMed: 16855860

Assembly members:

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:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MMP-12: FREMPGGPVWRKHYITYRIN NYTPDMNREDVDYAIRKAFQ VWSNVTPLKFSKINTGMADI LVVFARGAHGDFHAFDGKGG ILAHAFGPGSGIGGDAHFDE DEFWTTHSGGTNLFLTAVHE IGHSLGLGHSSDPKAVMFPT YKYVDINTFRLSADDIRGIQ SLYG
THP: GPXGPXGPXGPXGPPGVVGE QGEQGPXGPXGPXGPX

Data sets:
Data typeCount
13C chemical shifts635
15N chemical shifts165
1H chemical shifts953

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1MMP-121
2THP_12
3THP_22
4THP_32
5ZINC ION_13
6ZINC ION_23
7CALCIUM ION_14
8CALCIUM ION_24
9CALCIUM ION_34
10water5

Entities:

Entity 1, MMP-12 164 residues - 18235.561 Da.

1   PHEARGGLUMETPROGLYGLYPROVALTRP
2   ARGLYSHISTYRILETHRTYRARGILEASN
3   ASNTYRTHRPROASPMETASNARGGLUASP
4   VALASPTYRALAILEARGLYSALAPHEGLN
5   VALTRPSERASNVALTHRPROLEULYSPHE
6   SERLYSILEASNTHRGLYMETALAASPILE
7   LEUVALVALPHEALAARGGLYALAHISGLY
8   ASPPHEHISALAPHEASPGLYLYSGLYGLY
9   ILELEUALAHISALAPHEGLYPROGLYSER
10   GLYILEGLYGLYASPALAHISPHEASPGLU
11   ASPGLUPHETRPTHRTHRHISSERGLYGLY
12   THRASNLEUPHELEUTHRALAVALHISGLU
13   ILEGLYHISSERLEUGLYLEUGLYHISSER
14   SERASPPROLYSALAVALMETPHEPROTHR
15   TYRLYSTYRVALASPILEASNTHRPHEARG
16   LEUSERALAASPASPILEARGGLYILEGLN
17   SERLEUTYRGLY

Entity 2, THP_1 36 residues - 3291.483 Da.

1   GLYPROHYPGLYPROHYPGLYPROHYPGLY
2   PROHYPGLYPROPROGLYVALVALGLYGLU
3   GLNGLYGLUGLNGLYPROHYPGLYPROHYP
4   GLYPROHYPGLYPROHYP

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCUnprimedisotropicsample_conditions_Unprimed
2D 1H-15N HSQCPrimedisotropicsample_conditions_Primed
2D 1H-13C HSQCPrimedisotropicsample_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 HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks