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BMRB: 25766

2N6J

Solution structure of Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile

Authors

Banci, L., Cantini, F., Scarselli, M., Rubino, J.T., Martinelli, M.

Assembly

Zmp1

Entity

1. Zmp1 (polymer, Thiol state: all free), 195 monomers, 21601.01 Da Detail

GDSTTIQQNK DTLSQIVVFP TGNYDKNEAN AMVNRLANID GKYLNALKQN NLKIKLLSGK LTDEKEYAYL KGVVPKGWEG TGKTWDDVPG LGGSTVALRI GFSNKGKGHD AINLELHETA HAIDHIVLND ISKSAQFKQI FAKEGRSLGN VNYLGVYPEE FFAESFAYYY LNQDTNSKLK SACPQTYSFL QNLAK

2. ZINC ION (non-polymer), 65.409 Da
3. WATER (water), 18.015 Da

Total weight

21666.418 Da

Max. entity weight

21601.01 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:GLU160:OE1	2:ZN1:ZN
2	na	sing	1:HIS121:NE2	2:ZN1:ZN
3	na	sing	1:HIS117:NE2	2:ZN1:ZN
4	na	sing	2:ZN1:ZN	3:HOH1:O

Source organism

Clostridioides difficile

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.4 %, Completeness (bb): 95.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.4 % (2156 of 2284)	95.4 % (1131 of 1185)	91.8 % (809 of 881)	99.1 % (216 of 218)
Backbone	95.2 % (1104 of 1160)	96.8 % (389 of 402)	92.8 % (527 of 568)	98.9 % (188 of 190)
Sidechain	94.4 % (1229 of 1302)	94.8 % (742 of 783)	93.5 % (459 of 491)	100.0 % (28 of 28)
Aromatic	77.5 % (155 of 200)	85.0 % (85 of 100)	69.4 % (68 of 98)	100.0 % (2 of 2)
Methyl	96.7 % (205 of 212)	94.3 % (100 of 106)	99.1 % (105 of 106)

1. Zmp1

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	Zmp1	[U-100% 15N]	0.6 (±0.2) mM
2	Zmp1	[U-99% 13C; U-99% 15N]	0.5 (±0.2) mM
3	Zmp1	natural abundance	1 (±0.2) mM
4	Hepes	natural abundance	20 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	61.3 ppm	external	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0

Referencing offset: -0.31 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	61.3 ppm	external	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0

Referencing offset: -0.31 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	61.3 ppm	external	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	dioxane	methyl carbon	61.3 ppm	external	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0

Referencing offset: -0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N6J, Strand ID: A Detail

Release date

2016-01-10

Citation

Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile
Rubino, J.T., Martinelli, M., Cantini, F., Banci, L., Scarselli, M.
J. Biol. Inorg. Chem. (2015), 21, 185-196, PubMed 26711661 , DOI 10.1007/s00775-015-1319-6 , Abstract

Related entities 1. Zmp1, : 1 : 7 : 17 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC