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BMRB: 34282

6GRV

Cadmium(II) form of full-length metallothionein from Pseudomonas fluorescens Q2-87 (PflQ2 MT)

Authors

Habjanic, J., Zerbe, O., Freisinger, E.

Assembly

Metallothionein

Entity

1. Metallothionein, entity 1 (polymer), 81 monomers, 8812.508 Da Detail

NELRCGCPDC HCKVDPERVF NHDGEAYCSQ ACAEQHPNGE PCPAPDCHCE RSGKVGGRDI TNNQLDEALE ETFPASDPIS P

2. Metallothionein, entity CD (non-polymer), 112.411 × 4 Da

Total weight

9262.151 Da

Max. entity weight

8812.508 Da

Entity Connection

metal coordination 16 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS7:SG	2:CD1:CD
2	metal coordination	sing	1:CYS32:SG	2:CD1:CD
3	metal coordination	sing	1:HIS36:NE2	2:CD1:CD
4	metal coordination	sing	1:CYS49:SG	2:CD1:CD
5	metal coordination	sing	1:CYS10:SG	2:CD1:CD
6	metal coordination	sing	1:CYS42:SG	2:CD1:CD
7	metal coordination	sing	1:CYS47:SG	2:CD1:CD
8	metal coordination	sing	1:CYS49:SG	2:CD1:CD
9	metal coordination	sing	1:CYS10:SG	2:CD1:CD
10	metal coordination	sing	1:CYS12:SG	2:CD1:CD
11	metal coordination	sing	1:CYS28:SG	2:CD1:CD
12	metal coordination	sing	1:CYS42:SG	2:CD1:CD
13	metal coordination	sing	1:CYS5:SG	2:CD1:CD
14	metal coordination	sing	1:CYS10:SG	2:CD1:CD
15	metal coordination	sing	1:CYS28:SG	2:CD1:CD
16	metal coordination	sing	1:CYS32:SG	2:CD1:CD

Source organism

Pseudomonas fluorescens Q2-87

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.7 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.7 % (829 of 857)	98.0 % (442 of 451)	95.1 % (310 of 326)	96.2 % (77 of 80)
Backbone	96.4 % (451 of 468)	98.7 % (157 of 159)	94.9 % (225 of 237)	95.8 % (69 of 72)
Sidechain	97.6 % (453 of 464)	97.6 % (285 of 292)	97.6 % (160 of 164)	100.0 % (8 of 8)
Aromatic	81.8 % (36 of 44)	81.8 % (18 of 22)	81.8 % (18 of 22)
Methyl	100.0 % (48 of 48)	100.0 % (24 of 24)	100.0 % (24 of 24)

1. entity 1

NELRCGCPDC HCKVDPERVF NHDGEAYCSQ ACAEQHPNGE PCPAPDCHCE RSGKVGGRDI TNNQLDEALE ETFPASDPIS P

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.4 (±0.2), Details 0.5 mM [U-13C; U-15N] metallothionein, 2 mM cadmium ion, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.4 (±0.2), Details 1.5 mM metallothionein, 6 mM U-113CD cadmium ion, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	metallothionein	natural abundance	1.5 (±0.1) mM
6	cadmium ion	U-113CD	6 (±0.1) mM
7	TRIS	[U-2H]	50 (±1.0) mM
8	sodium chloride	natural abundance	50 (±1.0) mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	150.928 Hz	external	indirect	0.2514495
¹H	DSS	methyl protons	600.23 Hz	external	direct	1.0
¹⁵N	DSS	methyl protons	60.82078 Hz	external	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	150.928 Hz	external	indirect	0.2514495
¹H	DSS	methyl protons	600.23 Hz	external	direct	1.0
¹⁵N	DSS	methyl protons	60.82078 Hz	external	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	150.928 Hz	external	indirect	0.2514495
¹H	DSS	methyl protons	600.23 Hz	external	direct	1.0
¹⁵N	DSS	methyl protons	60.82078 Hz	external	indirect	0.1013291

Referencing offset: 0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	150.928 Hz	external	indirect	0.2514495
¹H	DSS	methyl protons	600.23 Hz	external	direct	1.0
¹⁵N	DSS	methyl protons	60.82078 Hz	external	indirect	0.1013291

Referencing offset: 0.28 ppm, Outliers: 3 Detail

Release date

2018-07-01

Citation

A histidine-rich Pseudomonas metallothionein with a disordered tail displays higher binding capacity for cadmium than zinc
Habjanic, J., Zerbe, O., Freisinger, E.
Metallomics. (2018), 10, 1415-1429, PubMed 30191219 , DOI 10.1039/c8mt00193f , Abstract

Entries sharing articles BMRB: 3 entries Detail

  BMRB: 34288 released on 2018-09-09
    Title Cadmium(II) form of shortened metallothionein from Pseudomonas fluorescens Q2-87 (residues: 1-52)
  BMRB: 34293 released on 2018-09-09
    Title Zn(II) form of shortened metallothionein from Pseudomonas fluorescens Q2-87 (residues 1-52)
  BMRB: 34289 released on 2018-07-02
    Title Cadmium(II) form of A44H mutant of shortened metallothionein from Pseudomonas fluorescens Q2-87 (residues 1-52)

Related entities 1. Metallothionein, entity 1, : 1 : 1 entities Detail

Experiments performed 17 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.4 (±0.2), Details 0.5 mM [U-13C; U-15N] metallothionein, 2 mM cadmium ion, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

2 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance (1H; 13C; 15N) with an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

7 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

8 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

9 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz CRYO TXI inverse triple-resonance (1H; 13C; 15N) with an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

13 2D 1H-113Cd HSQC-TOCSY

Instrument

Bruker AvanceII - 500 MHz CRYO 5 mm BBO probe with an actively shielded z-gradient coil

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 320 K, pH 7.4 (±0.2), Details 1.5 mM metallothionein, 6 mM U-113CD cadmium ion, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	metallothionein	natural abundance	1.5 (±0.1) mM
6	cadmium ion	U-113CD	6 (±0.1) mM
7	TRIS	[U-2H]	50 (±1.0) mM
8	sodium chloride	natural abundance	50 (±1.0) mM

14 1D 113Cd

Instrument

Bruker AvanceII - 500 MHz CRYO 5 mm BBO probe with an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
5	metallothionein	natural abundance	1.5 (±0.1) mM
6	cadmium ion	U-113CD	6 (±0.1) mM
7	TRIS	[U-2H]	50 (±1.0) mM
8	sodium chloride	natural abundance	50 (±1.0) mM

15 2D (HB)CB(CGCDCE)HE

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

16 2D (HB)CB(CGCD)HD

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

17 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil

Sample

#	Name	Isotope labeling	Concentration
1	metallothionein	[U-13C; U-15N]	0.5 (±0.1) mM
2	cadmium ion	natural abundance	2 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34282_6grv.nef
Input source #2: Coordindates	6grv.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)
1:5:CYS:SG	2:4:CD:CD	unknown	unknown	n/a
1:7:CYS:SG	2:1:CD:CD	unknown	unknown	n/a
1:10:CYS:SG	2:3:CD:CD	unknown	unknown	n/a
1:10:CYS:SG	2:4:CD:CD	unknown	unknown	n/a
1:10:CYS:SG	2:2:CD:CD	unknown	unknown	n/a
1:12:CYS:SG	2:3:CD:CD	unknown	unknown	n/a
1:28:CYS:SG	2:3:CD:CD	unknown	unknown	n/a
1:28:CYS:SG	2:4:CD:CD	unknown	unknown	n/a
1:32:CYS:SG	2:4:CD:CD	unknown	unknown	n/a
1:32:CYS:SG	2:1:CD:CD	unknown	unknown	n/a
1:36:HIS:NE2	2:1:CD:CD	unknown	unknown	n/a
1:42:CYS:SG	2:3:CD:CD	unknown	unknown	n/a
1:42:CYS:SG	2:2:CD:CD	unknown	unknown	n/a
1:47:CYS:SG	2:2:CD:CD	unknown	unknown	n/a
1:49:CYS:SG	2:2:CD:CD	unknown	unknown	n/a
1:49:CYS:SG	2:1:CD:CD	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CD	CADMIUM ION	None
B	2	CD	CADMIUM ION	None
B	3	CD	CADMIUM ION	None
B	4	CD	CADMIUM ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80-
NELRCGCPDCHCKVDPERVFNHDGEAYCSQACAEQHPNGEPCPAPDCHCERSGKVGGRDITNNQLDEALEETFPASDPISP
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NELRCGCPDCHCKVDPERVFNHDGEAYCSQACAEQHPNGEPCPAPDCHCERSGKVGGRDITNNQLDEALEETFPASDPISP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	81	0	0	100.0

Content subtype: combined_34282_6grv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	16		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	835		100.0 (chain: A, length: 81)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1154 (1)	noe	97.5 (chain: A, length: 81)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	74 (74)	.	69.1 (chain: A, length: 81)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 441
  - ¹³C chemical shifts: 309
  - ¹⁵N chemical shifts: 85
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
11	HIS	ND1	201.32
11	HIS	NE2	175.972
22	HIS	ND1	203.573
22	HIS	NE2	175.53
36	HIS	HD1	13.33
36	HIS	ND1	173.925
36	HIS	NE2	225.689
48	HIS	ND1	182.279
48	HIS	NE2	174.791

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	451	440	97.6
¹³C chemical shifts	326	309	94.8
¹⁵N chemical shifts	84	77	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	159	156	98.1
¹³C chemical shifts	162	149	92.0
¹⁵N chemical shifts	72	69	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	292	284	97.3
¹³C chemical shifts	164	160	97.6
¹⁵N chemical shifts	12	8	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	24	100.0
¹³C chemical shifts	24	24	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	18	81.8
¹³C chemical shifts	22	18	81.8

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 97.5%
- Total number of restraints: 1147
- Weight of restraints: 1.0 (1147)
- Potential type of restraints: square-well-parabolic (1147)
- Range of distance target values: 1.11, 2.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 69.1%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords METAL BINDING PROTEIN, cadmium ion, metallothionein

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Found 1 Document (0.579 seconds)

BMRB: 34282

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 3 entries Detail

Related entities 1. Metallothionein, entity 1, : 1 : 1 entities Detail

Experiments performed 17 experiments Detail

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NMR combined restraints 4 contents Detail