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BMRB: 26047

2ND5

Lysine dimethylated FKBP12

Authors

Hattori, Y., Sebera, J., Sychrovsky, V., Furuita, K., Sugiki, T., Ohki, I., Ikegami, T., Kobayashi, N., Tanaka, Y., Fujiwara, T., Kojima, C.

Assembly

Lysine dimethylated FKBP12

Entity

1. Lysine dimethylated FKBP12 (polymer), 111 monomers, 12416.24 Da Detail

GPSMGVQVET ISPGDGRTFP XRGQTCVVHY TGMLEDGXXF DSSRDRNXPF XFMLGXQEVI RGWEEGVAQM SVGQRAXLTI SPDYAYGATG HPGIIPPHAT LVFDVELLXL E

Formula weight

12416.24 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.9 %, Completeness: 98.2 %, Completeness (bb): 98.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.2 % (1122 of 1143)	97.6 % (575 of 589)	98.9 % (447 of 452)	98.0 % (100 of 102)
Backbone	98.2 % (591 of 602)	97.6 % (207 of 212)	98.6 % (291 of 295)	97.9 % (93 of 95)
Sidechain	98.4 % (620 of 630)	97.6 % (368 of 377)	99.6 % (245 of 246)	100.0 % (7 of 7)
Aromatic	98.0 % (96 of 98)	98.0 % (48 of 49)	97.9 % (47 of 48)	100.0 % (1 of 1)
Methyl	100.0 % (108 of 108)	100.0 % (54 of 54)	100.0 % (54 of 54)

1. entity

GPSMGVQVET ISPGDGRTFP XRGQTCVVHY TGMLEDGXXF DSSRDRNXPF XFMLGXQEVI RGWEEGVAQM SVGQRAXLTI SPDYAYGATG HPGIIPPHAT LVFDVELLXL E

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.06 ppm, Outliers: 5 Detail

LACS Plot; CO

Referencing offset: 0.39 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2ND5, Strand ID: A Detail

Release date

2016-05-12

Citation

NMR Observation of Protein Surface Salt Bridges at Neutral pH
Hattori, Y., Sebera, J., Sychrovsky, V., Furuita, K., Sugiki, T., Ohki, I., Ikegami, T., Kobayashi, N., Tanaka, Y., Fujiwara, T., Kojima, C.
J. Am. Chem. Soc.

Related entities 1. Lysine dimethylated FKBP12, : 1 : 92 : 249 entities Detail

Interaction partners 1. Lysine dimethylated FKBP12, : 22 interactors Detail

More details for 22 interactors identified by 14 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

6 3D HNCACB

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

7 3D HN(CA)CO

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

8 3D HNCO

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

10 3D C(CO)NH

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

11 3D HC(CO)NH

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

12 3D HCCH-TOCSY

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

13 3D 1H-15N TOCSY

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

14 3D 1H-15N NOESY

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

15 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

16 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance III - 800 MHz with a TXI cryogenic probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 303 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium chloride	natural abundance		30 mM
3	DTT	natural abundance		3 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_26047_2nd5.nef
Input source #2: Coordindates	2nd5.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)
1:20:PRO:C	1:21:MLY:N	unknown	unknown	n/a
1:21:MLY:C	1:22:ARG:N	unknown	unknown	n/a
1:37:GLY:C	1:38:MLY:N	unknown	unknown	n/a
1:38:MLY:C	1:39:MLY:N	unknown	unknown	n/a
1:39:MLY:C	1:40:PHE:N	unknown	unknown	n/a
1:47:ASN:C	1:48:MLY:N	unknown	unknown	n/a
1:48:MLY:C	1:49:PRO:N	unknown	unknown	n/a
1:50:PHE:C	1:51:MLY:N	unknown	unknown	n/a
1:51:MLY:C	1:52:PHE:N	unknown	unknown	n/a
1:55:GLY:C	1:56:MLY:N	unknown	unknown	n/a
1:56:MLY:C	1:57:GLN:N	unknown	unknown	n/a
1:76:ALA:C	1:77:MLY:N	unknown	unknown	n/a
1:77:MLY:C	1:78:LEU:N	unknown	unknown	n/a
1:108:LEU:C	1:109:MLY:N	unknown	unknown	n/a
1:109:MLY:C	1:110:LEU:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	17	MLY	N-DIMETHYL-LYSINE	Assigned chemical shifts, Coordinates
A	34	MLY	N-DIMETHYL-LYSINE	Assigned chemical shifts, Coordinates
A	35	MLY	N-DIMETHYL-LYSINE	Assigned chemical shifts, Coordinates
A	44	MLY	N-DIMETHYL-LYSINE	Assigned chemical shifts, Coordinates
A	47	MLY	N-DIMETHYL-LYSINE	Assigned chemical shifts, Coordinates
A	52	MLY	N-DIMETHYL-LYSINE	Assigned chemical shifts, Coordinates
A	73	MLY	N-DIMETHYL-LYSINE	Assigned chemical shifts, Coordinates
A	105	MLY	N-DIMETHYL-LYSINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

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

-100-------
LVFDVELLXLE
|||||||||||
LVFDVELLXLE
-------110-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	111	0	0	100.0

Content subtype: combined_26047_2nd5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	15		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1278		99.1 (chain: A, length: 111)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3588 (1)	noe	91.0 (chain: A, length: 111)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	124 (124)	.	79.3 (chain: A, length: 111)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 675
  - ¹³C chemical shifts: 494
  - ¹⁵N chemical shifts: 109
- 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

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: 111, Sequence coverage: 91.0%
- Total number of restraints: 3588
- Weight of restraints: 1.0 (3588)
- Potential type of restraints: upper-bound-parabolic (3588)
- Range of distance target values: 2.51, 6.0 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 79.3%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NMR, lysine, methylation, salt bridge