BMRBj - BMREntryMaster

Found 1 Document (0.576 seconds)

BMRB: 16025

2KAK

Solution structure of the beta-E domain of wheat Ec-1 metallothionein

Authors

Peroza, E.A., Schmucki, R., Guntert, P., Freisinger, E., Zerbe, O.

Assembly

Ec-1 metallothionein

Entity

1. Ec-1 metallothionein (polymer, Thiol state: all other bound), 53 monomers, 5078.567 Da Detail

GEHTTCGCGE HCGCNPCACG REGTPSGRAN RRANCSCGAA CNCASCGSAT APG

2. ZN (non-polymer), 65.409 × 4 Da

Total weight

5340.203 Da

Max. entity weight

5078.567 Da

Source organism

Triticum aestivum

Exptl. method

solution NMR

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.3 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	97.3 % (287 of 295)	98.3 % (237 of 241)	92.6 % (50 of 54)
Backbone	100.0 % (163 of 163)	100.0 % (113 of 113)	100.0 % (50 of 50)
Sidechain	93.9 % (124 of 132)	96.9 % (124 of 128)	0.0 % (0 of 4)
Aromatic	100.0 % (4 of 4)	100.0 % (4 of 4)
Methyl	100.0 % (12 of 12)	100.0 % (12 of 12)

1. Ec-1 metallothionein

GEHTTCGCGE HCGCNPCACG REGTPSGRAN RRANCSCGAA CNCASCGSAT APG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 300 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	1.0 mM
2	TRIS	natural abundance	15.0 mM
3	NaCl	natural abundance	50.0 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 300 K, pH 6.8

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 15N]	1.0 mM
5	TRIS	natural abundance	15.0 mM
6	NaCl	natural abundance	50.0 mM

Protein Blocks Logo

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

Release date

2009-04-13

Citation

The beta(E)-domain of wheat E(c)-1 metallothionein: a metal-binding domain with a distinctive structure
Peroza, E.A., Schmucki, R., Guntert, P., Freisinger, E., Zerbe, O.
J. Mol. Biol. (2009), 387, 207-218, PubMed 19361445 , DOI 10.1016/j.jmb.2009.01.035 , Abstract

Related entities 1. Ec-1 metallothionein, : 1 : 2 : 11 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16025_2kak.nef
Input source #2: Coordindates	2kak.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	Error

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)
1:3:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:6:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:6:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:8:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:11:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:12:CYS:SG	2:4:ZN:ZN	unknown	unknown	n/a
1:14:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:17:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:19:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:35:CYS:SG	2:4:ZN:ZN	unknown	unknown	n/a
1:37:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:37:CYS:SG	2:4:ZN:ZN	unknown	unknown	n/a
1:41:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:43:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:46:CYS:SG	2:4:ZN:ZN	unknown	unknown	n/a
1:46:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	Distance restraints
B	2	ZN	ZINC ION	None
B	3	ZN	ZINC ION	None
B	4	ZN	ZINC ION	None

Sequence alignments

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

--------40--------50--------60--------70--------80---
GEHTTCGCGEHCGCNPCACGREGTPSGRANRRANCSCGAACNCASCGSATAPG
|||||||||||||||||||||||||||||||||||||||||||||||||||||
GEHTTCGCGEHCGCNPCACGREGTPSGRANRRANCSCGAACNCASCGSATAPG
--------10--------20--------30--------40--------50---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	53	0	0	100.0

Content subtype: combined_16025_2kak.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	16		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	287		100.0 (chain: A, length: 53)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	708 (1)	noe	98.1 (chain: A, length: 53)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Error	122 (1)	undefined	24.5 (chain: A, length: 53), 25.0 (chain: B, length: 4)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 237
  - ¹⁵N chemical shifts: 50
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	241	236	97.9
¹⁵N chemical shifts	58	50	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	113	112	99.1
¹⁵N chemical shifts	50	50	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	128	124	96.9
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 98.1%
- Total number of restraints: 707
- Weight of restraints: 1.0 (707)
- Potential type of restraints: upper-bound-parabolic (707)
- Range of distance target values: 2.48, 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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Error
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 24.5%
    - Entity_assembly_ID: B, Chain length: 4, Sequence coverage: 25.0%
  - Total number of restraints: 122
  - Weight of restraints: 1.0 (122)
  - Potential type of restraints: upper-bound-parabolic (122)
  - Range of distance target values: 2.0, 4.0 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Keywords metallothionein, NMR, solution structure, wheat Ec-1, Zn binding

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.576 seconds)

BMRB: 16025

Sample #1

Sample #2

Related entities 1. Ec-1 metallothionein, : 1 : 2 : 11 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail