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Found 1 Document (2.878 seconds)

BMRB: 18509

2LU5

Structure and chemical shifts of Cu(I),Zn(II) superoxide dismutase by solid-state NMR

Authors

Knight, M.J., Pell, A.J., Bertini, I., Felli, I.C., Gonnelli, L., Pierattelli, R., Herrmann, T., Emsley, L., Pintacuda, G.

Assembly

Cu(I),Zn(II) superoxide dismutase

Entity

1. Superoxide dismutase C6A-C111S thermostable mutant (polymer, Thiol state: all disulfide bound), 153 monomers, 15756.23 Da Detail

ATKAVAVLKG DGPVQGIINF EQKESNGPVK VWGSIKGLTE GLHGFHVHEF GDNTAGCTSA GPHFNPLSRK HGGPKDEERH VGDLGNVTAD KDGVADVSIE DSVISLSGDH SIIGRTLVVH EKADDLGKGG NEESTKTGNA GSRLACGVIG IAQ

2. COPPER (II) ION (non-polymer), 63.546 Da

Total weight

15819.776 Da

Max. entity weight

15756.23 Da

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 34.8 %, Completeness (bb): 59.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	34.8 % (564 of 1621)	21.2 % (177 of 833)	39.9 % (251 of 629)	85.5 % (136 of 159)
Backbone	59.5 % (540 of 908)	46.9 % (153 of 326)	57.8 % (251 of 434)	91.9 % (136 of 148)
Sidechain	3.3 % (28 of 841)	4.7 % (24 of 507)	1.2 % (4 of 323)	0.0 % (0 of 11)
Aromatic	3.6 % (3 of 84)	7.1 % (3 of 42)	0.0 % (0 of 41)	0.0 % (0 of 1)
Methyl	1.2 % (2 of 166)	2.4 % (2 of 83)	0.0 % (0 of 83)

1. Superoxide dismutase C6A-C111S thermostable mutant

ATKAVAVLKG DGPVQGIINF EQKESNGPVK VWGSIKGLTE GLHGFHVHEF GDNTAGCTSA GPHFNPLSRK HGGPKDEERH VGDLGNVTAD KDGVADVSIE DSVISLSGDH SIIGRTLVVH EKADDLGKGG NEESTKTGNA GSRLACGVIG IAQ

Show sample condition

Sample

Solvent system 100% H2O, Pressure 1 atm, Temperature 286 K, pH 5

#	Name	Isotope labeling	Concentration
1	Superoxide dismutase C6A/C111S thermostable mutant	[U-13C; U-15N; U-2H]	3.5 mg
2	Sodium Citrate	natural abundance	20 mM
3	Polyethylene Glycol 6000	natural abundance	.20 w/v

Protein Blocks Logo

Calculated from 19 models in PDB: 2LU5, Strand ID: A Detail

Release date

2012-08-28

Citation

Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR
Knight, M.J., Pell, A.J., Bertini, I., Felli, I.C., Gonnelli, L., Pierattelli, R., Herrmann, T., Emsley, L., Pintacuda, G.
Proc. Natl. Acad. Sci. U. S. A. (2012), 109, 11095-11100, PubMed 22723345 , DOI 10.1073/pnas.1204515109 , Abstract

Related entities 1. Superoxide dismutase C6A-C111S thermostable mutant, : 1 : 4 : 2 : 88 : 154 entities Detail

Interaction partners 1. Superoxide dismutase C6A-C111S thermostable mutant, : 26 interactors Detail

More details for 26 interactors identified by 11 citations

Experiments performed 6 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18509_2lu5.nef
Input source #2: Coordindates	2lu5.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:57:CYS:SG	A:146:CYS:SG	unknown, CA 49.088 ppm	unknown, CA 51.077 ppm	2.051

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)
1:139:ASN:O	2:1:CU:CU	unknown	unknown	n/a
1:46:HIS:O	2:1:CU:CU	unknown	unknown	n/a
1:118:VAL:O	2:1:CU:CU	unknown	unknown	n/a
1:124:ASP:OD1	2:1:CU:CU	unknown	unknown	n/a
1:124:ASP:OD2	2:1:CU:CU	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CU	COPPER (II) ION	Distance restraints

Sequence alignments

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

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

-------110-------120-------130-------140-------150---
DSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||
DSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	153	0	0	100.0

Content subtype: combined_18509_2lu5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	517		97.4 (chain: A, length: 153)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	442 (1)	noe	88.2 (chain: A, length: 153)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	4262 (1)	undefined	100.0 (chain: A, length: 153)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	15985 (1)	undefined	100.0 (chain: A, length: 153), 100.0 (chain: B, length: 1)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	27072 (1)	hbond	56.2 (chain: A, length: 153)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	Warning	880 (869)	.	100.0 (chain: A, length: 153)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 97.4%
- Total number of assignments
  - ¹³C chemical shifts: 245
  - ¹H chemical shifts: 136
  - ¹⁵N chemical shifts: 136
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	629	245	39.0
¹H chemical shifts	833	136	16.3
¹⁵N chemical shifts	163	136	83.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	306	245	80.1
¹H chemical shifts	326	136	41.7
¹⁵N chemical shifts	148	136	91.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	323	0	0.0
¹H chemical shifts	507	0	0.0
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	83	0	0.0
¹H chemical shifts	83	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	41	0	0.0
¹H chemical shifts	42	0	0.0
¹⁵N chemical shifts	1	0	0.0

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: 153, Sequence coverage: 88.2%
- Total number of restraints: 442
- Weight of restraints: 1.0 (442)
- Potential type of restraints: square-well-parabolic (442)
- Range of distance target values: 2.33, 4.2 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 100.0%
  - Total number of restraints: 4262
  - Weight of restraints: 1.0 (4262)
  - Potential type of restraints: square-well-parabolic (4262)
  - Range of distance target values: 3.24, 6.6 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: OK
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 100.0%
      - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
    - Total number of restraints: 15985
    - Weight of restraints: 1.0 (15985)
    - Potential type of restraints: square-well-parabolic (15985)
    - Range of distance target values: 2.1, 61.59 (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
    - Saveframe: CNS/XPLOR_distance_constraints_5
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 56.2%
        --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ATKAVAVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIE ||||||||| ||||| ||| |||||||| ||||| ||||||| |||| ||| ||||| ||| |||| ||||| .TKAVAVLKG...VQGII.FEQ......VKVWGSIK.LTEGL.GFHVHEF...TAGC.........LSR.....KDEER....LGN....KDGV.DVSIE --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130-------140-------150--- DSVISLSGDHSIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ ||||| |||||||||| |||||||||| DSVIS......IIGRTLVVHE.....................RLACGVIGIA -------110-------120-------130-------140-------150--
      - Total number of restraints: 27072
        Total hydrogen bond restraints: 27072
        O...h-N (too far!): 188
        O...H-x (too far!): 188
        Long range: 26696
        O...h-N (too far!): 13348
        O...H-x (too far!): 13348
      - Weight of restraints: 1.0 (27072)
        Total hydrogen bond restraints: 1.0 (27072)
        O...h-N (too far!): 1.0 (188)
        O...H-x (too far!): 1.0 (188)
        Long range: 1.0 (26696)
        O...h-N (too far!): 1.0 (13348)
        O...H-x (too far!): 1.0 (13348)
      - Potential type of restraints: square-well-parabolic (27072)
        Total hydrogen bond restraints: square-well-parabolic (27072)
        O...h-N (too far!): square-well-parabolic (188)
        O...H-x (too far!): square-well-parabolic (188)
        Long range: square-well-parabolic (26696)
        O...h-N (too far!): square-well-parabolic (13348)
        O...H-x (too far!): square-well-parabolic (13348)
      - Range of distance target values: 3.4, 4.38 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 100.0%
- Total number of restraints: 869
- Total number of restraints per polymer type: 869
- Weight of restraints: 1.0 (869)
- Potential type of restraints: square-well-parabolic (869)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Metalloprotein, Microcrystalline, Paramagnetic, Protein, Solid-state NMR

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Found 1 Document (2.878 seconds)

BMRB: 18509

Sample

Related entities 1. Superoxide dismutase C6A-C111S thermostable mutant, : 1 : 4 : 2 : 88 : 154 entities Detail

Interaction partners 1. Superoxide dismutase C6A-C111S thermostable mutant, : 26 interactors Detail

Experiments performed 6 experiments Detail

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NMR combined restraints 7 contents Detail