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BMRB: 34293

6GW8

Zn(II) form of shortened metallothionein from Pseudomonas fluorescens Q2-87 (residues 1-52)

Authors

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

Assembly

metallothionein

Entity

1. metallothionein, entity 1 (polymer, Thiol state: all other bound), 52 monomers, 5759.259 Da Detail

NELRCGCPDC HCKVDPERVF NHDGEAYCSQ ACAEQHPNGE PCPAPDCHCE RS

2. metallothionein, entity ZN (non-polymer), 65.409 × 3 Da

Total weight

5955.486 Da

Max. entity weight

5759.259 Da

Entity Connection

na 12 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS7:SG	2:ZN1:ZN
2	na	sing	1:CYS32:SG	2:ZN1:ZN
3	na	sing	1:HIS36:NE2	2:ZN1:ZN
4	na	sing	1:CYS49:SG	2:ZN1:ZN
5	na	sing	1:CYS10:SG	2:ZN1:ZN
6	na	sing	1:CYS42:SG	2:ZN1:ZN
7	na	sing	1:CYS47:SG	2:ZN1:ZN
8	na	sing	1:CYS49:SG	2:ZN1:ZN
9	na	sing	1:CYS5:SG	2:ZN1:ZN
10	na	sing	1:CYS12:SG	2:ZN1:ZN
11	na	sing	1:CYS28:SG	2:ZN1:ZN
12	na	sing	1:CYS32:SG	2:ZN1:ZN

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: 93.2 %, Completeness (bb): 89.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (508 of 545)	95.5 % (275 of 288)	91.7 % (189 of 206)	86.3 % (44 of 51)
Backbone	89.0 % (267 of 300)	90.1 % (91 of 101)	89.5 % (137 of 153)	84.8 % (39 of 46)
Sidechain	98.3 % (289 of 294)	98.4 % (184 of 187)	98.0 % (100 of 102)	100.0 % (5 of 5)
Aromatic	97.1 % (33 of 34)	100.0 % (17 of 17)	94.1 % (16 of 17)
Methyl	100.0 % (20 of 20)	100.0 % (10 of 10)	100.0 % (10 of 10)

1. entity 1

NELRCGCPDC HCKVDPERVF NHDGEAYCSQ ACAEQHPNGE PCPAPDCHCE RS

Show sample condition

Sample

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, 1.5 mM ZINC 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	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: 0.25 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: 0.25 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: 0.16 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: 0.91 ppm, Outliers: 2 Detail

Release date

2018-09-09

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: 34289 released on 2018-07-02
    Title Cadmium(II) form of A44H mutant of shortened metallothionein from Pseudomonas fluorescens Q2-87 (residues 1-52)
  BMRB: 34282 released on 2018-07-01
    Title Cadmium(II) form of full-length metallothionein from Pseudomonas fluorescens Q2-87 (PflQ2 MT)

Related entities 1. metallothionein, entity 1, : 1 : 2 : 1 : 5 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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, 1.5 mM ZINC 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

4 3D HNCO

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

6 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

12 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	ZINC ION	natural abundance	1.5 (±0.1) mM
3	TRIS	[U-2H]	50 (±1.0) mM
4	sodium chloride	natural abundance	50 (±1.0) mM

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz CRYO TCI inverse triple-resonance (1H; 13C; 15N) 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	ZINC ION	natural abundance	1.5 (±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_34293_6gw8.nef
Input source #2: Coordindates	6gw8.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	2:3:ZN:ZN	unknown	unknown	n/a
1:7:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:10:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:12:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:28:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:32:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:32:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:36:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:42:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:47:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:49:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:49:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None
B	3	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--
NELRCGCPDCHCKVDPERVFNHDGEAYCSQACAEQHPNGEPCPAPDCHCERS
||||||||||||||||||||||||||||||||||||||||||||||||||||
NELRCGCPDCHCKVDPERVFNHDGEAYCSQACAEQHPNGEPCPAPDCHCERS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	52	0	0	100.0

Content subtype: combined_34293_6gw8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	12		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	514		100.0 (chain: A, length: 52)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	780 (1)	noe	98.1 (chain: A, length: 52)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	72 (72)	.	94.2 (chain: A, length: 52)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 275
  - ¹³C chemical shifts: 188
  - ¹⁵N chemical shifts: 51
- 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	222.056
11	HIS	NE2	178.223
22	HIS	ND1	216.638
22	HIS	NE2	177.084
36	HIS	ND1	174.256
36	HIS	NE2	223.655
48	HIS	ND1	190.727
48	HIS	NE2	179.41

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	288	275	95.5
¹³C chemical shifts	206	188	91.3
¹⁵N chemical shifts	54	43	79.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	92	91.1
¹³C chemical shifts	104	89	85.6
¹⁵N chemical shifts	46	38	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	187	183	97.9
¹³C chemical shifts	102	99	97.1
¹⁵N chemical shifts	8	5	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	16	94.1
¹³C chemical shifts	17	15	88.2

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: 52, Sequence coverage: 98.1%
- Total number of restraints: 778
- Weight of restraints: 1.0 (778)
- Potential type of restraints: square-well-parabolic (778)
- Range of distance target values: 1.22, 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: 52, Sequence coverage: 94.2%
- Total number of restraints: 72
- Total number of restraints per polymer type: 72
- Weight of restraints: 1.0 (72)
- Potential type of restraints: square-well-parabolic (72)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords METAL BINDING PROTEIN, metallothionein, zinc(II) ion

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Found 1 Document (0.612 seconds)

BMRB: 34293

Sample

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 : 2 : 1 : 5 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 4 contents Detail