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BMRB: 34072

5ML1

NMR Structure of the Littorina littorea metallothionein, a snail MT folding into three distinct domains

Authors

Baumann, C., Beil, A., Jurt, S., Zerbe, O.

Assembly

Putative metallothionein

Entity

1. Putative metallothionein (polymer), 102 monomers, 10183.61 Da Detail

GSMSSVFGAG CTDVCKQTPC GCATSGCNCT DDCKCQSCKY GAGCTDTCKQ TPCGCGSGCN CKEDCRCQSC STACKCAAGS CKCGKGCTGP DSCKCDRSCS CK

2. CADMIUM ION (non-polymer), 867.5768 × 9 Da

Total weight

17991.8 Da

Max. entity weight

10183.61 Da

Entity Connection

na 36 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS11:SG	2:CD1:CD
2	na	sing	1:CYS15:SG	2:CD1:CD
3	na	sing	1:CYS15:SG	2:CD1:CD
4	na	sing	1:CYS20:SG	2:CD1:CD
5	na	sing	1:CYS22:SG	2:CD1:CD
6	na	sing	1:CYS27:SG	2:CD1:CD
7	na	sing	1:CYS29:SG	2:CD1:CD
8	na	sing	1:CYS29:SG	2:CD1:CD
9	na	sing	1:CYS33:SG	2:CD1:CD
10	na	sing	1:CYS35:SG	2:CD1:CD
11	na	sing	1:CYS38:SG	2:CD1:CD
12	na	sing	1:CYS38:SG	2:CD1:CD
13	na	sing	1:CYS44:SG	2:CD1:CD
14	na	sing	1:CYS48:SG	2:CD1:CD
15	na	sing	1:CYS48:SG	2:CD1:CD
16	na	sing	1:CYS53:SG	2:CD1:CD
17	na	sing	1:CYS55:SG	2:CD1:CD
18	na	sing	1:CYS59:SG	2:CD1:CD
19	na	sing	1:CYS61:SG	2:CD1:CD
20	na	sing	1:CYS61:SG	2:CD1:CD
21	na	sing	1:CYS65:SG	2:CD1:CD
22	na	sing	1:CYS67:SG	2:CD1:CD
23	na	sing	1:CYS70:SG	2:CD1:CD
24	na	sing	1:CYS70:SG	2:CD1:CD
25	na	sing	1:CYS74:SG	2:CD1:CD
26	na	sing	1:CYS76:SG	2:CD1:CD
27	na	sing	1:CYS81:SG	2:CD1:CD
28	na	sing	1:CYS83:SG	2:CD1:CD
29	na	sing	1:CYS87:SG	2:CD1:CD
30	na	sing	1:CYS93:SG	2:CD1:CD
31	na	sing	1:CYS93:SG	2:CD1:CD
32	na	sing	1:CYS95:SG	2:CD1:CD
33	na	sing	1:CYS95:SG	2:CD1:CD
34	na	sing	1:CYS99:SG	2:CD1:CD
35	na	sing	1:CYS101:SG	2:CD1:CD
36	na	sing	1:CYS101:SG	2:CD1:CD

Source organism

Littorina littorea

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 84.3 %, Completeness (bb): 80.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.3 % (817 of 969)	93.4 % (470 of 503)	68.4 % (247 of 361)	95.2 % (100 of 105)
Backbone	80.7 % (489 of 606)	95.3 % (205 of 215)	65.1 % (190 of 292)	94.9 % (94 of 99)
Sidechain	91.6 % (413 of 451)	92.0 % (265 of 288)	90.4 % (142 of 157)	100.0 % (6 of 6)
Aromatic	0.0 % (0 of 18)	0.0 % (0 of 9)	0.0 % (0 of 9)
Methyl	100.0 % (38 of 38)	100.0 % (19 of 19)	100.0 % (19 of 19)

1. Putative metallothionein

GSMSSVFGAG CTDVCKQTPC GCATSGCNCT DDCKCQSCKY GAGCTDTCKQ TPCGCGSGCN CKEDCRCQSC STACKCAAGS CKCGKGCTGP DSCKCDRSCS CK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.2) K, pH 7.0 (±0.05), Details 0.5 mM [U-99% 15N] Metallothionein from Littorina Littorea, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Metallothionein from Littorina Littorea	[U-99% 15N]	0.5 mM
2	TRIS	natural abundance	20 mM
3	TCEP	natural abundance	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.2) K, pH 7.0 (±0.05), Details 0.5 mM [U-99% 13C; U-99% 15N] Metallothionein from Littorina Littorea, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.2) K, pH 7.0 (±0.05), Details 2 mM [U-99% 15N]113Cd Metallothionein from Littorina Littorea, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	Metallothionein from Littorina Littorea	[U-99% 15N]113Cd	2 mM
12	TRIS	natural abundance	20 mM
13	TCEP	natural abundance	1 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	internal	direct	1.0
¹H	TSP	methyl protons	internal	direct	1.0
¹⁵N	TSP	methyl protons	internal	indirect	0.101329

Referencing offset: 0.27 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	internal	direct	1.0
¹H	TSP	methyl protons	internal	direct	1.0
¹⁵N	TSP	methyl protons	internal	indirect	0.101329

Referencing offset: 0.27 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	internal	direct	1.0
¹H	TSP	methyl protons	internal	direct	1.0
¹⁵N	TSP	methyl protons	internal	indirect	0.101329

Referencing offset: -0.02 ppm, Outliers: 7 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5ML1, Strand ID: A Detail

Release date

2016-12-08

Citation

Structural Adaptation of a Protein to Increased Metal Stress: NMR Structure of a Marine Snail Metallothionein with an Additional Domain
Baumann, C., Beil, A., Jurt, S., Niederwanger, M., Palacios, O., Capdevila, M., Atrian, S., Dallinger, R., Zerbe, O.
Angew. Chem Int Ed Engl. (2017), 56, 4617-4622, PubMed 28332759 , DOI 10.1002/anie.201611873 , Abstract

Related entities 1. Putative metallothionein, : 1 : 3 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.2) K, pH 7.0 (±0.05), Details 0.5 mM [U-99% 15N] Metallothionein from Littorina Littorea, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Metallothionein from Littorina Littorea	[U-99% 15N]	0.5 mM
2	TRIS	natural abundance	20 mM
3	TCEP	natural abundance	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.2) K, pH 7.0 (±0.05), Details 0.5 mM [U-99% 13C; U-99% 15N] Metallothionein from Littorina Littorea, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

4 3D HNCACB

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
1	Metallothionein from Littorina Littorea	[U-99% 15N]	0.5 mM
2	TRIS	natural abundance	20 mM
3	TCEP	natural abundance	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

8 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

10 113Cd-1H HSQC

Instrument

Bruker AvanceII - 500 MHz with cryo probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.2) K, pH 7.0 (±0.05), Details 2 mM [U-99% 15N]113Cd Metallothionein from Littorina Littorea, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	Metallothionein from Littorina Littorea	[U-99% 15N]113Cd	2 mM
12	TRIS	natural abundance	20 mM
13	TCEP	natural abundance	1 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

11 113Cd-HSQC-TOCSY

Instrument

Bruker AvanceII - 500 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
11	Metallothionein from Littorina Littorea	[U-99% 15N]113Cd	2 mM
12	TRIS	natural abundance	20 mM
13	TCEP	natural abundance	1 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

12 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz with cryo probe

Sample

#	Name	Isotope labeling	Concentration
6	Metallothionein from Littorina Littorea	[U-99% 13C; U-99% 15N]	0.5 mM
7	TRIS	natural abundance	20 mM
8	TCEP	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34072_5ml1.nef
Input source #2: Coordindates	5ml1.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:11:CYS:SG	2:7:CD:CD	unknown	unknown	n/a
1:15:CYS:SG	2:9:CD:CD	unknown	unknown	n/a
1:15:CYS:SG	2:7:CD:CD	unknown	unknown	n/a
1:20:CYS:SG	2:9:CD:CD	unknown	unknown	n/a
1:22:CYS:SG	2:8:CD:CD	unknown	unknown	n/a
1:27:CYS:SG	2:8:CD:CD	unknown	unknown	n/a
1:29:CYS:SG	2:8:CD:CD	unknown	unknown	n/a
1:29:CYS:SG	2:7:CD:CD	unknown	unknown	n/a
1:33:CYS:SG	2:7:CD:CD	unknown	unknown	n/a
1:35:CYS:SG	2:9:CD:CD	unknown	unknown	n/a
1:38:CYS:SG	2:8:CD:CD	unknown	unknown	n/a
1:38:CYS:SG	2:9:CD:CD	unknown	unknown	n/a
1:44:CYS:SG	2:5:CD:CD	unknown	unknown	n/a
1:48:CYS:SG	2:4:CD:CD	unknown	unknown	n/a
1:48:CYS:SG	2:5:CD:CD	unknown	unknown	n/a
1:53:CYS:SG	2:4:CD:CD	unknown	unknown	n/a
1:55:CYS:SG	2:6:CD:CD	unknown	unknown	n/a
1:59:CYS:SG	2:6:CD:CD	unknown	unknown	n/a
1:61:CYS:SG	2:6:CD:CD	unknown	unknown	n/a
1:61:CYS:SG	2:5:CD:CD	unknown	unknown	n/a
1:65:CYS:SG	2:5:CD:CD	unknown	unknown	n/a
1:67:CYS:SG	2:4:CD:CD	unknown	unknown	n/a
1:70:CYS:SG	2:6:CD:CD	unknown	unknown	n/a
1:70:CYS:SG	2:4:CD:CD	unknown	unknown	n/a
1:74:CYS:SG	2:1:CD:CD	unknown	unknown	n/a
1:76:CYS:SG	2:1:CD:CD	unknown	unknown	n/a
1:81:CYS:SG	2:2:CD:CD	unknown	unknown	n/a
1:83:CYS:SG	2:3:CD:CD	unknown	unknown	n/a
1:87:CYS:SG	2:2:CD:CD	unknown	unknown	n/a
1:93:CYS:SG	2:1:CD:CD	unknown	unknown	n/a
1:93:CYS:SG	2:2:CD:CD	unknown	unknown	n/a
1:95:CYS:SG	2:2:CD:CD	unknown	unknown	n/a
1:95:CYS:SG	2:3:CD:CD	unknown	unknown	n/a
1:99:CYS:SG	2:3:CD:CD	unknown	unknown	n/a
1:101:CYS:SG	2:1:CD:CD	unknown	unknown	n/a
1:101:CYS:SG	2:3:CD:CD	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CD	CADMIUM ION	None
B	2	CD	CADMIUM ION	None
B	3	CD	CADMIUM ION	None
B	4	CD	CADMIUM ION	None
B	5	CD	CADMIUM ION	None
B	6	CD	CADMIUM ION	None
B	7	CD	CADMIUM ION	None
B	8	CD	CADMIUM ION	None
B	9	CD	CADMIUM ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GSMSSVFGAGCTDVCKQTPCGCATSGCNCTDDCKCQSCKYGAGCTDTCKQTPCGCGSGCNCKEDCRCQSCSTACKCAAGSCKCGKGCTGPDSCKCDRSCS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSMSSVFGAGCTDVCKQTPCGCATSGCNCTDDCKCQSCKYGAGCTDTCKQTPCGCGSGCNCKEDCRCQSCSTACKCAAGSCKCGKGCTGPDSCKCDRSCS

--
CK
||
CK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	102	0	0	100.0

Content subtype: combined_34072_5ml1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	36		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	808		96.1 (chain: A, length: 102)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1885 (1)	noe	96.1 (chain: A, length: 102)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 96.1%
- Total number of assignments
  - ¹H chemical shifts: 469
  - ¹³C chemical shifts: 240
  - ¹⁵N chemical shifts: 99
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	503	469	93.2
¹³C chemical shifts	361	240	66.5
¹⁵N chemical shifts	107	99	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	215	204	94.9
¹³C chemical shifts	204	98	48.0
¹⁵N chemical shifts	99	93	93.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	288	265	92.0
¹³C chemical shifts	157	142	90.4
¹⁵N chemical shifts	8	6	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	19	95.0
¹³C chemical shifts	20	19	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	0	0.0
¹³C chemical shifts	9	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 96.1%
- Total number of restraints: 1885
- Weight of restraints: 1.0 (1885)
- Potential type of restraints: upper-bound-parabolic (1885)
- Range of distance target values: 2.36, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords METAL BINDING PROTEIN, NMR metallothionein metal cluster metalloprotein

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Found 1 Document (0.681 seconds)

BMRB: 34072

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Putative metallothionein, : 1 : 3 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 3 contents Detail