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BMRB: 25527

2N0K

Chemical shift assignments and structure of the alpha-crystallin domain from human, HSPB5

Authors

Rajagopal, P., Klevit, R.E., Shi, L., Baker, D.

Assembly

alpha-crystallin domain from human, HSPB5

Entity

1. alpha-crystallin domain from human, HSPB5 (polymer, Thiol state: not present), 89 monomers, 10181.34 × 2 Da Detail

GLSEMRLEKD RFSVNLDVKH FSPEELKVKV LGDVIEVHGK HEERQDEHGF ISREFHRKYR IPADVDPLTI TSSLSSDGVL TVDGPRKQV

Total weight

20362.68 Da

Max. entity weight

10181.34 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 92.4 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.4 % (967 of 1047)	94.4 % (518 of 549)	88.8 % (364 of 410)	96.6 % (85 of 88)
Backbone	96.4 % (507 of 526)	96.1 % (173 of 180)	96.6 % (252 of 261)	96.5 % (82 of 85)
Sidechain	89.7 % (542 of 604)	93.5 % (345 of 369)	83.6 % (194 of 232)	100.0 % (3 of 3)
Aromatic	79.4 % (54 of 68)	94.1 % (32 of 34)	64.7 % (22 of 34)
Methyl	96.9 % (93 of 96)	100.0 % (48 of 48)	93.8 % (45 of 48)

1. HSPB5-ACD

GLSEMRLEKD RFSVNLDVKH FSPEELKVKV LGDVIEVHGK HEERQDEHGF ISREFHRKYR IPADVDPLTI TSSLSSDGVL TVDGPRKQV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	HSPB5-ACD	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	.1 mM
5	PMSF	natural abundance	1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5, Details For measuring Residual Dipolar Coupling

#	Name	Isotope labeling	Concentration
11	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	100 mM
14	EDTA	natural abundance	.1 mM
15	PMSF	natural abundance	1 mM
16	Pf1 phage	natural abundance	14 mg/mL

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
17	HSPB5-ACD	[U-100% 13C; U-100% 15N]	1.0 mM
18	sodium phosphate	natural abundance	50 mM
19	sodium chloride	natural abundance	100 mM
20	EDTA	natural abundance	.1 mM
21	PMSF	natural abundance	1 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
22	HSPB5-ACD	[U-100% 13C; U-100% 15N; 50% 2H]	1.0 mM
23	sodium phosphate	natural abundance	50 mM
24	sodium chloride	natural abundance	100 mM
25	EDTA	natural abundance	.1 mM
26	PMSF	natural abundance	1 mM

LACS Plot; CA

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

Referencing offset: 0.4 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.4 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.24 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.91 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 9 models in PDB: 2N0K, Strand ID: A, B Detail

Release date

2015-05-31

Citation 1

A conserved histidine modulates HSPB5 structure to trigger chaperone activity in response to stress-related acidosis
Rajagopal, P., Tse, E., Borst, A.J., Delbecq, S.P., Shi, L., Dove, K.D., Baker, D., Southworth, D.R., Klevit, R.E.
Elife (2015), 4, PubMed 25962097 , DOI 10.7554/eLife.07304 , Abstract

Show more 3 citaions

Citation 2

alphaB-crystallin: a hybrid solid-state/solution-state NMR investigation reveals structural aspects of the heterogeneous oligomer
Jehle, S., van Rossum, B., Stout, J.R., Noguchi, S.M., Falber, K., Rehbein, K.J., Oschkinat, H., Klevit, R.E., Rajagopal, P.J.
J. Mol. Biol. (2009), 385, 1481-1497, PubMed 19041879 , DOI 10.1016/j.jmb.2008.10.097 , Abstract

Citation 3

Solid-state NMR and SAXS studies provide a structural basis for the activation of alphaB-crystallin oligomers
Jehle, S., Rajagopal, P., Bardiaux, B.J., Markovic, S.J., Kuhne, R., Stout, J.R., Higman, V., Klevit, R.E., van Rossum, B.J., Oschkinat, H.
Nat. Struct. Mol. Biol. (2010), 17, 1037-1042, PubMed 20802487 , DOI 10.1038/nsmb.1891 , Abstract

Citation 4

N-terminal domain of alphaB-crystallin provides a conformational switch for multimerization and structural heterogeneity
Jehle, S., Vollmar, B., Bardiaux, B.J., Dove, K.K., Rajagopal, P., Gonen, T.J., Oschkinat, H., Klevit, R.E.
Proc. Natl. Acad. Sci. U. S. A. (2011), 108, 6409-6414, PubMed 21464278 , DOI 10.1073/pnas.1014656108 , Abstract

Hide non-primary 3 citaions

Related entities 1. alpha-crystallin domain from human, HSPB5, : 1 : 8 : 203 entities Detail

Interaction partners 1. alpha-crystallin domain from human, HSPB5, : 17 interactors Detail

More details for 17 interactors identified by 10 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	HSPB5-ACD	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	.1 mM
5	PMSF	natural abundance	1 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	HSPB5-ACD	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	.1 mM
5	PMSF	natural abundance	1 mM

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
17	HSPB5-ACD	[U-100% 13C; U-100% 15N]	1.0 mM
18	sodium phosphate	natural abundance	50 mM
19	sodium chloride	natural abundance	100 mM
20	EDTA	natural abundance	.1 mM
21	PMSF	natural abundance	1 mM

6 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
17	HSPB5-ACD	[U-100% 13C; U-100% 15N]	1.0 mM
18	sodium phosphate	natural abundance	50 mM
19	sodium chloride	natural abundance	100 mM
20	EDTA	natural abundance	.1 mM
21	PMSF	natural abundance	1 mM

7 3D HNCACB

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

9 3D HNCO

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

10 3D HNCA

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

11 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

12 3D HN(COCA)CB

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	HSPB5-ACD	[U-100% 13C; U-100% 15N; U-80% 2H]	0.6 mM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	EDTA	natural abundance	.1 mM
10	PMSF	natural abundance	1 mM

13 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
17	HSPB5-ACD	[U-100% 13C; U-100% 15N]	1.0 mM
18	sodium phosphate	natural abundance	50 mM
19	sodium chloride	natural abundance	100 mM
20	EDTA	natural abundance	.1 mM
21	PMSF	natural abundance	1 mM

14 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
22	HSPB5-ACD	[U-100% 13C; U-100% 15N; 50% 2H]	1.0 mM
23	sodium phosphate	natural abundance	50 mM
24	sodium chloride	natural abundance	100 mM
25	EDTA	natural abundance	.1 mM
26	PMSF	natural abundance	1 mM

15 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.5

#	Name	Isotope labeling	Concentration
22	HSPB5-ACD	[U-100% 13C; U-100% 15N; 50% 2H]	1.0 mM
23	sodium phosphate	natural abundance	50 mM
24	sodium chloride	natural abundance	100 mM
25	EDTA	natural abundance	.1 mM
26	PMSF	natural abundance	1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25527_2n0k.nef
Input source #2: Coordindates	2n0k.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

-----70--------80--------90-------100-------110-------120-------130-------140-------150--
GLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVDGPRKQV
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVDGPRKQV
--------10--------20--------30--------40--------50--------60--------70--------80---------

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

-----70--------80--------90-------100-------110-------120-------130-------140-------150--
GLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVDGPRKQV
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVDGPRKQV
--------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	89	0	0	100.0
B	B	89	0	0	100.0

Content subtype: combined_25527_2n0k.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	HSPB5_ACD_chemical_shifts	Warning	978		98.9 (chain: A, length: 89)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2153 (1)	noe	97.8 (chain: A, length: 89), 97.8 (chain: B, length: 89)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	226 (226)	.	80.9 (chain: A, length: 89), 80.9 (chain: B, length: 89)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	154 (154)	.	86.5 (chain: A, length: 89)

Assigned chemical shifts

Saveframe: HSPB5_ACD_chemical_shifts

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 98.9%

-----70--------80--------90-------100-------110-------120-------130-------140-------150--
GLSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVDGPRKQV
 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
.LSEMRLEKDRFSVNLDVKHFSPEELKVKVLGDVIEVHGKHEERQDEHGFISREFHRKYRIPADVDPLTITSSLSSDGVLTVDGPRKQV

Total number of assignments
- ¹H chemical shifts: 524
- ¹³C chemical shifts: 359
- ¹⁵N chemical shifts: 95

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
83	HIS	ND1	230.2
83	HIS	NE2	176.8
101	HIS	ND1	231.6
101	HIS	NE2	173.1
104	HIS	ND1	168.8
104	HIS	NE2	249.7
111	HIS	ND1	235.4
111	HIS	NE2	174.97
119	HIS	ND1	210.0
119	HIS	NE2	180.2
132	THR	HG1	5.9
144	THR	HG1	5.62

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	549	522	95.1
¹³C chemical shifts	410	359	87.6
¹⁵N chemical shifts	95	85	89.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	180	175	97.2
¹³C chemical shifts	178	165	92.7
¹⁵N chemical shifts	85	82	96.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	369	347	94.0
¹³C chemical shifts	232	194	83.6
¹⁵N chemical shifts	10	3	30.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	49	100.0
¹³C chemical shifts	49	46	93.9

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	31	91.2
¹³C chemical shifts	34	22	64.7

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: 89, Sequence coverage: 97.8%
  - Entity_assembly_ID: B, Chain length: 89, Sequence coverage: 97.8%
- Total number of restraints: 2121
- Weight of restraints: 1.0 (2121)
- Potential type of restraints: square-well-parabolic (2121)
- Range of distance target values: 2.11, 5.1 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 80.9%
  - Entity_assembly_ID: B, Chain length: 89, Sequence coverage: 80.9%
- Total number of restraints: 226
- Total number of restraints per polymer type: 226
- Weight of restraints: 1.0 (226)
- Potential type of restraints: square-well-parabolic (226)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 86.5%
- Total number of restraints: 154
- Potential type of restraints: undefined (154)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords ACD, Protein, crystallin, human

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Found 1 Document (2.063 seconds)

BMRB: 25527

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. alpha-crystallin domain from human, HSPB5, : 1 : 8 : 203 entities Detail

Interaction partners 1. alpha-crystallin domain from human, HSPB5, : 17 interactors Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail