BMRBj - BMREntryMaster

Found 1 Document (1.475 seconds)

BMRB: 6617

4FU4

Backbone 1H,15N assignment of the C-terminal haemopexin-like domain of matrix metalloproteinase MMP-13 (collagenase-3)

Authors

Jacobs, D.M., Grimme, S., Elshorst, B., Pescatore, B., Vogtherr, M., Saxena, K., Betz, M., Schieborr, U., Langer, T., Schwalbe, H., Fiebig, K.

Assembly

C-terminal haemopexin-like domain of matrix metalloproteinase MMP-13 (collagenase-3)

Entity

1. c-terminal haemopexin-like domain of matrix metalloproteinase MMP-13 (polymer, Thiol state: all disulfide bound), 207 monomers, 24152.12 Da Detail

LYGPGDEDPN PKHPKTPDKC DPSLSLDAIT SLRGETMIFK DRFFWRLHPQ QVDAELFLTK SFWPELPNRI DAAYEHPSHD LIFIFRGRKF WALNGYDILE GYPKKISELG LPKEVKKISA AVHFEDTGKT LLFSGNQVWR YDDTNHIMDK DYPRLIEEDF PGIGDKVDAV YEKNGYIYFF NGPIQFEYSI WSNRIVRVMP ANSILWC

2. CA (non-polymer), 40.078 × 2 Da

Total weight

24232.275 Da

Max. entity weight

24152.12 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS20:SG	1:CYS207:SG

Source organism

Homo sapiens

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.0 %, Completeness: 35.0 %, Completeness (bb): 63.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	35.0 % (890 of 2540)	19.1 % (254 of 1328)	47.3 % (474 of 1002)	77.1 % (162 of 210)
Backbone	63.3 % (766 of 1210)	39.2 % (161 of 411)	73.0 % (444 of 608)	84.3 % (161 of 191)
Sidechain	17.3 % (263 of 1524)	10.1 % (93 of 917)	28.7 % (169 of 588)	5.3 % (1 of 19)
Aromatic	4.7 % (15 of 316)	6.3 % (10 of 158)	3.3 % (5 of 152)	0.0 % (0 of 6)
Methyl	15.8 % (31 of 196)	13.3 % (13 of 98)	18.4 % (18 of 98)

1. c-terminal haemopexin-like domain of matrix metalloproteinase MMP-13

Show sample condition

Sample

Temperature 298 K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Concentration
1	matrix metalloproteinase MMP-13	[U-13C; U-15N; U-50% 2H]	0.7 mM
2	BisTris		20 mM
3	Na2SO4		200 mM
4	CaCl2		5 mM
5	Arginine		10 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.69 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.69 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -1.68 ppm, Outliers: 1 Detail

Release date

2005-10-25

Citation 1

Backbone NMR assignment of the C-terminal haemopexin-like domain (HPLD) of human matrix metalloproteinase MMP-13
Jacobs, D.M., Grimme, S., Elshorst, B., Pescatore, B., Vogtherr, M., Betz, M., Schieborr, U., Langer, T., Saxena, K., Schwalbe, H., Fiebig, K.
J. Biomol. NMR (2005), 32, 337-337, PubMed 16211490 , DOI 10.1007/s10858-005-0463-7 , Abstract

Show more 1 citaion

Citation 2

The helping hand of collagenase-3 (MMP-13): 2.7 A crystal structure of its C-terminal haemopexin-like domain
Gomis-Ruth, F.
J. Mol. Biol. (1996), 264, 556-566, PubMed 8969305 , DOI 10.1006/jmbi.1996.0661 , Abstract

Hide non-primary 1 citaion

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 6584 released on 2005-10-24
    Title Backbone assignment of the E2 ubiquitin conjugating enzyme UbcH5alpha
  Swiss-Prot: P45452 released on 1995-11-01
    Title MMP13_HUMAN Entity Collagenase 3

Related entities 1. c-terminal haemopexin-like domain of matrix metalloproteinase MMP-13, : 1 : 5 : 180 entities Detail

Experiments performed 6 experiments Detail

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6617_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:20:CYS:SG	1:207:CYS:SG	unknown, CA 59.012 ppm	oxidized, CA 57.789, CB 41.55 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr6617_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	736		86.0 (chain: 1, length: 207)
1	Chemical shift references	chemical_shift_referencing	OK	3		No information

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 207, Sequence coverage: 86.0%
- Total number of assignments
  - ¹³C chemical shifts: 440
  - ¹H chemical shifts: 137
  - ¹⁵N chemical shifts: 159
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1002	440	43.9
¹H chemical shifts	1328	137	10.3
¹⁵N chemical shifts	220	159	72.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	414	302	72.9
¹H chemical shifts	411	137	33.3
¹⁵N chemical shifts	191	159	83.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	588	138	23.5
¹H chemical shifts	917	0	0.0
¹⁵N chemical shifts	29	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	101	8	7.9
¹H chemical shifts	101	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	152	0	0.0
¹H chemical shifts	158	0	0.0
¹⁵N chemical shifts	6	0	0.0

Keywords Haemopexin-like domain, Matrix metalloproteinase, NMR backbone assignment

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Found 1 Document (1.475 seconds)

BMRB: 6617

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

Related entities 1. c-terminal haemopexin-like domain of matrix metalloproteinase MMP-13, : 1 : 5 : 180 entities Detail

Experiments performed 6 experiments Detail

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Chemical shift validation 4 contents Detail