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Found 1 Document (0.949 seconds)

BMRB: 30087

5JWJ

NMR solution structure of a thermophilic lysine methyl transferase from Sulfolobus islandicus

Authors

de Lichtenberg, C., Stiefler-Jensen, D., Schwarz-Linnet, T., She, Q., Teilum, K.

Assembly

Protein-lysine N-methyltransferase (E.C.2.1.1.-)

Entity

1. Protein-lysine N-methyltransferase (E.C.2.1.1.-) (polymer), 172 monomers, 19388.09 Da Detail

MSYVPHVPYV PTPEKVVRRM LEIAKVSQDD IVYALGCGDG RIIITAAKDF NVKKAVGVEI NDERIREALA NIEKNGVTGR ASIVKGNFFE VDISEATVVT MFLLTNVNEM LKPKLEKELK PGTRVVSHEF EIRGWNPKEV IKVEDGNMNH TVYLYVIGEH KAAALEHHHH HH

Formula weight

19388.09 Da

Source organism

Sulfolobus islandicus REY15A

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.9 %, Completeness: 79.6 %, Completeness (bb): 89.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.6 % (1606 of 2018)	78.0 % (815 of 1045)	80.3 % (639 of 796)	85.9 % (152 of 177)
Backbone	89.8 % (914 of 1018)	89.7 % (312 of 348)	89.3 % (451 of 505)	91.5 % (151 of 165)
Sidechain	71.8 % (834 of 1161)	72.2 % (503 of 697)	73.0 % (330 of 452)	8.3 % (1 of 12)
Aromatic	31.0 % (44 of 142)	33.8 % (24 of 71)	27.1 % (19 of 70)	100.0 % (1 of 1)
Methyl	88.2 % (194 of 220)	89.1 % (98 of 110)	87.3 % (96 of 110)

1. Protein-lysine N-methyltransferase

MSYVPHVPYV PTPEKVVRRM LEIAKVSQDD IVYALGCGDG RIIITAAKDF NVKKAVGVEI NDERIREALA NIEKNGVTGR ASIVKGNFFE VDISEATVVT MFLLTNVNEM LKPKLEKELK PGTRVVSHEF EIRGWNPKEV IKVEDGNMNH TVYLYVIGEH KAAALEHHHH HH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details 1 mM [U-100% 13C; U-100% 15N] aKMT_D34A, 20 mM Na-acetate, 0.5 mM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details 1 mM [U-100% 13C; U-100% 15N] aKMT_D34A, 20 mM Na-acetate, 0.5 mM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	DSS	natural abundance	0.5 mM
7	Na-acetate	natural abundance	20 mM
8	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details 1 mM [U-100% 13C; U-100% 15N] aKMT_D34A, 20 mM Na-acetate, 0.5 mM DSS, 0.123 M C12E5, 0.111 M hexanol, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	C12E5	natural abundance	0.123 M
12	DSS	natural abundance	0.5 mM
13	Na-acetate	natural abundance	20 mM
14	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
15	hexanol	natural abundance	0.111 M
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.28 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2016-05-23

Citation

NMR solution structure of a thermophilic lysine methyl transferase from Sulfolobus islandicus
de Lichtenberg, C., Stiefler-Jensen, D., Schwarz-Linnet, T., She, Q., Teilum, K.

Related entities 1. Protein-lysine N-methyltransferase (E.C.2.1.1.-), : 1 : 3 : 14 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent DD2 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details 1 mM [U-100% 13C; U-100% 15N] aKMT_D34A, 20 mM Na-acetate, 0.5 mM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 3D HNCO

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 3D HNCA

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D HN(CO)CA

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 3D HN(CA)CO

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

6 3D CBCA(CO)NH

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

7 3D HNCACB

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

8 3D 1H-15N NOESY

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

9 3D 1H-15N TOCSY

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

10 2D IPAP HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.5 mM
2	Na-acetate	natural abundance	20 mM
3	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

11 3D HCCH-TOCSY aromatic

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	DSS	natural abundance	0.5 mM
7	Na-acetate	natural abundance	20 mM
8	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

12 3D HCCH-TOCSY

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	DSS	natural abundance	0.5 mM
7	Na-acetate	natural abundance	20 mM
8	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

13 2D IPAP HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5, Details 1 mM [U-100% 13C; U-100% 15N] aKMT_D34A, 20 mM Na-acetate, 0.5 mM DSS, 0.123 M C12E5, 0.111 M hexanol, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	C12E5	natural abundance	0.123 M
12	DSS	natural abundance	0.5 mM
13	Na-acetate	natural abundance	20 mM
14	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
15	hexanol	natural abundance	0.111 M
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

14 3D 1H-13C NOESY aliphatic

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	DSS	natural abundance	0.5 mM
7	Na-acetate	natural abundance	20 mM
8	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

15 3D 1H-13C NOESY aromatic

Instrument

Agilent DD2 - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	DSS	natural abundance	0.5 mM
7	Na-acetate	natural abundance	20 mM
8	aKMT_D34A	[U-100% 13C; U-100% 15N]	1 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, RDC restraints	combined_30087_5jwj.nef
Input source #2: Coordindates	5jwj.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

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

-------110-------120-------130-------140-------150-------160-------170--
MFLLTNVNEMLKPKLEKELKPGTRVVSHEFEIRGWNPKEVIKVEDGNMNHTVYLYVIGEHKAAALEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MFLLTNVNEMLKPKLEKELKPGTRVVSHEFEIRGWNPKEVIKVEDGNMNHTVYLYVIGEHKAAALEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	172	0	0	100.0

Content subtype: combined_30087_5jwj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1588		90.7 (chain: A, length: 172)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3777 (1)	noe	86.6 (chain: A, length: 172)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	251 (251)	.	85.5 (chain: A, length: 172)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	108 (108)	.	62.8 (chain: A, length: 172)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 90.7%
- Total number of assignments
  - ¹³C chemical shifts: 631
  - ¹H chemical shifts: 803
  - ¹⁵N chemical shifts: 154
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	PRO	N	109.982
11	PRO	N	133.622
121	PRO	N	137.692
137	PRO	N	138.999

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	796	631	79.3
¹H chemical shifts	1045	803	76.8
¹⁵N chemical shifts	185	150	81.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	344	308	89.5
¹H chemical shifts	348	312	89.7
¹⁵N chemical shifts	165	149	90.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	452	323	71.5
¹H chemical shifts	697	491	70.4
¹⁵N chemical shifts	20	1	5.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	115	96	83.5
¹H chemical shifts	115	99	86.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	70	17	24.3
¹H chemical shifts	71	22	31.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 86.6%
- Total number of restraints: 3772
- Weight of restraints: 1.0 (3772)
- Potential type of restraints: square-well-parabolic (3772)
- Range of distance target values: 2.1, 3.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 85.5%
- Total number of restraints: 251
- Total number of restraints per polymer type: 251
- Weight of restraints: 1.0 (251)
- Potential type of restraints: square-well-parabolic (251)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 172, Sequence coverage: 62.8%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MSYVPHVPYVPTPEKVVRRMLEIAKVSQDDIVYALGCGDGRIIITAAKDFNVKKAVGVEINDERIREALANIEKNGVTGRASIVKGNFFEVDISEATVVT
     |   | | |||  | | ||||||| ||| || ||| || ||||| ||||  | ||| |    ||| | ||||||||||||| || ||||||| ||
.....H...V.T.EKV..R.L.IAKVSQD.IVY.LG.GDG.II.TAAKD.NVKK..G.EIN.E....ALA.I.KNGVTGRASIVKG.FF.VDISEAT.VT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140-------150-------160-------170--
MFLLTNVNEMLKPKLEKELKPGTRVVSHEFEIRGWNPKEVIKVEDGNMNHTVYLYVIGEHKAAALEHHHHHH
         ||  | ||||| |||||| |||||||| ||  | ||||||||| |||| | ||          
.........ML..K.EKELK.GTRVVS.EFEIRGWN.KE..K.EDGNMNHTV.LYVI.E.KA          
-------110-------120-------130-------140-------150-------160--

Total number of restraints: 108
Potential type of restraints: undefined (108)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords lysine methyl transferase, thermophilic, transferase

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Found 1 Document (0.949 seconds)

BMRB: 30087

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Protein-lysine N-methyltransferase (E.C.2.1.1.-), : 1 : 3 : 14 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail