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BMRB: 18794

2M05

Structure of module 2 from the E1 domain of C. elegans APL-1

Authors

Hinds, M.G., Leong, S.

Assembly

module 2 from the E1 domain of C. elegans APL-1

Entity

1. module 2 from the E1 domain of C. elegans APL-1 (polymer, Thiol state: all disulfide bound), 65 monomers, 7417.353 Da Detail

EACQFSHVNS RDQCNDYQHW KDEAGKQCKT KKSKGNKDMI VRSFAVLEPC ALDMFTGVEF VCCPN

Formula weight

7417.353 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS63:SG
2	disulfide	sing	1:CYS14:SG	1:CYS50:SG
3	disulfide	sing	1:CYS28:SG	1:CYS62:SG

Source organism

Caenorhabditis elegans

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.6 %, Completeness (bb): 99.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.6 % (715 of 756)	99.0 % (393 of 397)	87.8 % (252 of 287)	97.2 % (70 of 72)
Backbone	99.0 % (382 of 386)	100.0 % (131 of 131)	99.0 % (190 of 192)	96.8 % (61 of 63)
Sidechain	91.4 % (395 of 432)	98.5 % (262 of 266)	79.0 % (124 of 157)	100.0 % (9 of 9)
Aromatic	48.5 % (33 of 68)	94.1 % (32 of 34)	0.0 % (0 of 33)	100.0 % (1 of 1)
Methyl	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (22 of 22)

1. entity

EACQFSHVNS RDQCNDYQHW KDEAGKQCKT KKSKGNKDMI VRSFAVLEPC ALDMFTGVEF VCCPN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.4 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.4 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.25 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M05, Strand ID: A Detail

Release date

2013-10-20

Citation

Quantification of copper binding to amyloid precursor protein domain 2 and its Caenorhabditis elegans ortholog. Implications for biological function
Leong, S., Young, T.R., Barnham, K.J., Wedd, A.G., Hinds, M.G., Xiao, Z., Cappai, R.
Metallomics. (2014), 6, 105-116, PubMed 24276282 , DOI 10.1039/c3mt00258f , Abstract

Related entities 1. module 2 from the E1 domain of C. elegans APL-1, : 1 : 2 : 41 entities Detail

Interaction partners 1. module 2 from the E1 domain of C. elegans APL-1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

12 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details residues 133-196 of C. elegans APL-1

#	Name	Isotope labeling	Type	Concentration
1	APL-1	natural abundance		0.5 mM
2	APL-1	[U-100% 15N]		0.5 mM
3	APL-1	[U-100% 13C; U-100% 15N]		0.5 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18794_2m05.nef
Input source #2: Coordindates	2m05.cif
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)
A:135:CYS:SG	A:195:CYS:SG	oxidized, CA 57.975, CB 46.35 ppm	oxidized, CA 53.131, CB 45.381 ppm	2.021
A:146:CYS:SG	A:182:CYS:SG	oxidized, CA 56.038, CB 41.021 ppm	oxidized, CA 54.585, CB 46.35 ppm	2.026
A:160:CYS:SG	A:194:CYS:SG	oxidized, CA 55.069, CB 33.271 ppm	oxidized, CA 51.194, CB 38.599 ppm	2.02

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

None

Non-standard residues

None

Sequence alignments

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

-----140-------150-------160-------170-------180-------190-------
EACQFSHVNSRDQCNDYQHWKDEAGKQCKTKKSKGNKDMIVRSFAVLEPCALDMFTGVEFVCCPN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EACQFSHVNSRDQCNDYQHWKDEAGKQCKTKKSKGNKDMIVRSFAVLEPCALDMFTGVEFVCCPN
--------10--------20--------30--------40--------50--------60-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	65	0	0	100.0

Content subtype: combined_18794_2m05.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	711		100.0 (chain: A, length: 65)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1271 (1)	noe	100.0 (chain: A, length: 65)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	102 (101)	.	95.4 (chain: A, length: 65)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 391
  - ¹³C chemical shifts: 252
  - ¹⁵N chemical shifts: 68
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 100.0%
- Total number of restraints: 1267
- Weight of restraints: 1.0 (1267)
- Potential type of restraints: square-well-parabolic (1267)
- Range of distance target values: 2.08, 3.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 95.4%
- Total number of restraints: 101
- Total number of restraints per polymer type: 101
- Weight of restraints: 1.0 (101)
- Potential type of restraints: square-well-parabolic (101)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Amyloid Precursor Protein, Apl-1, domain