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BMRB: 25241

2MV3

The N-domain of the AAA metalloproteinase Yme1 from Saccharomyces cerevisiae

Authors

Scharfenberg, F., Serek-Heuberger, J., Martin, J., Lupas, A.N., Coles, M.

Assembly

N-domain of the AAA metalloproteinase Yme1

Entity

1. N-domain of the AAA metalloproteinase Yme1 (polymer, Thiol state: all free), 88 monomers, 10041.12 Da Detail

MVAVSHAMLA TREQEANKDL TSPDAQAAFY KLLLQSNYPQ YVVSRFETPG IASSPECMEL YMEALQRIGR HSEADAVRQN LEHHHHHH

Formula weight

10041.12 Da

Source organism

Saccharomyces cerevisiae S288C

Exptl. method

Refine. method

simulated annealing, NOESY back-calculation

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.8 %, Completeness: 79.8 %, Completeness (bb): 77.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.8 % (805 of 1009)	81.3 % (425 of 523)	81.4 % (320 of 393)	64.5 % (60 of 93)
Backbone	77.9 % (405 of 520)	79.3 % (138 of 174)	80.2 % (210 of 262)	67.9 % (57 of 84)
Sidechain	83.0 % (477 of 575)	82.2 % (287 of 349)	86.2 % (187 of 217)	33.3 % (3 of 9)
Aromatic	61.9 % (52 of 84)	61.9 % (26 of 42)	61.9 % (26 of 42)
Methyl	93.2 % (82 of 88)	90.9 % (40 of 44)	95.5 % (42 of 44)

1. Yme1-N

MVAVSHAMLA TREQEANKDL TSPDAQAAFY KLLLQSNYPQ YVVSRFETPG IASSPECMEL YMEALQRIGR HSEADAVRQN LEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
1	Yme1-N	[U-100% 15N]		0.5 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		300 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.41 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: 0.41 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 23 models in PDB: 2MV3, Strand ID: A Detail

Release date

2016-09-21

Citation

Structure and evolution of N-domains in AAA metalloproteases
Scharfenberg, F., Serek-Heuberger, J., Coles, M., Hartmann, M.D., Habeck, M., Martin, J., Lupas, A.N., Alva, V.
J. Mol. Biol. (2015), 427, 910-923, PubMed 25576874 , DOI 10.1016/j.jmb.2014.12.024 , Abstract

Related entities 1. N-domain of the AAA metalloproteinase Yme1, : 1 : 2 : 3 entities Detail

Interaction partners 1. N-domain of the AAA metalloproteinase Yme1, : 6 interactors Detail

More details for 6 interactors identified by 4 citations

Experiments performed 13 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

2 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

3 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

4 3D CCH NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

5 3D CNH NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
1	Yme1-N	[U-100% 15N]		0.5 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		300 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

8 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
1	Yme1-N	[U-100% 15N]		0.5 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		300 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

9 3D HNHB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
1	Yme1-N	[U-100% 15N]		0.5 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		300 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

10 3D 3JHBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

11 3D NNH NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
1	Yme1-N	[U-100% 15N]		0.5 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		300 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

12 3D HN(CA)NNH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

13 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.9

#	Name	Isotope labeling	Type	Concentration
6	FtsH-N	[U-100% 13C; U-100% 15N]		0.5 mM
7	TRIS	natural abundance		20 mM
8	sodium chloride	natural abundance		300 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25241_2mv3.nef
Input source #2: Coordindates	2mv3.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--100-------110-------120-------130-------140-------150-------160-------170-------180---
MVAVSHAMLATREQEANKDLTSPDAQAAFYKLLLQSNYPQYVVSRFETPGIASSPECMELYMEALQRIGRHSEADAVRQNLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVAVSHAMLATREQEANKDLTSPDAQAAFYKLLLQSNYPQYVVSRFETPGIASSPECMELYMEALQRIGRHSEADAVRQNLEHHHHHH
--------10--------20--------30--------40--------50--------60--------70--------80--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	88	0	0	100.0

Content subtype: combined_25241_2mv3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	800		89.8 (chain: A, length: 88)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	523 (1)	noe	85.2 (chain: A, length: 88)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	52 (1)	hbond	78.4 (chain: A, length: 88)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	260 (260)	.	100.0 (chain: A, length: 88)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 89.8%
- Total number of assignments
  - ¹H chemical shifts: 426
  - ¹³C chemical shifts: 318
  - ¹⁵N chemical shifts: 56
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 85.2%
- Total number of restraints: 523
- Weight of restraints: 1.0 (523)
- Potential type of restraints: square-well-parabolic (523)
- Range of distance target values: 1.35, 6.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 78.4%
  - Total number of restraints: 52
  - Weight of restraints: 1.0 (52)
  - Potential type of restraints: square-well-parabolic (52)
  - Range of distance target values: 2.2, 2.2 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 100.0%
- Total number of restraints: 260
- Total number of restraints per polymer type: 260
- Weight of restraints: 1.0 (260)
- Potential type of restraints: square-well-parabolic (260)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords AAA ATPase, metalloprotease, substrate recognition domain