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Found 1 Document (0.498 seconds)

BMRB: 30239

5UNK

NMR structure of the RED subdomain of the Sleeping Beauty transposase

Authors

Konnova, T.A., Singer, C.M., Nesmelova, I.V.

Assembly

Uncharacterized protein

Entity

1. Uncharacterized protein (polymer, Thiol state: not present), 62 monomers, 7106.284 Da Detail

ASMVLSPRDE RTLVRKVQIN PRTTAKDLVK MLEETGTKVS ISTVKRVLYR HNLKGRSARK LE

Formula weight

7106.284 Da

Source organism

Oncorhynchus mykiss

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 76.2 %, Completeness (bb): 81.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.2 % (566 of 743)	84.5 % (332 of 393)	59.9 % (172 of 287)	98.4 % (62 of 63)
Backbone	81.0 % (298 of 368)	96.8 % (120 of 124)	64.7 % (119 of 184)	98.3 % (59 of 60)
Sidechain	74.9 % (326 of 435)	78.8 % (212 of 269)	68.1 % (111 of 163)	100.0 % (3 of 3)
Aromatic	50.0 % (6 of 12)	66.7 % (4 of 6)	33.3 % (2 of 6)
Methyl	79.3 % (65 of 82)	92.7 % (38 of 41)	65.9 % (27 of 41)

1. entity 1

ASMVLSPRDE RTLVRKVQIN PRTTAKDLVK MLEETGTKVS ISTVKRVLYR HNLKGRSARK LE

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 293 K, pH 5, Details 2 mg/mL [U-13C; U-15N] RED subdomain of the Sleeping Beauty transposase, 20 mM MES, 650 mM sodium sulfate, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	RED subdomain of the Sleeping Beauty transposase	[U-13C; U-15N]	2 mg/mL
3	sodium sulfate	natural abundance	650 mM

Sample #2

Solvent system 100% D2O, Pressure 1 null, Temperature 293 K, pH 5, Details 2 mg/mL [U-13C; U-15N] RED subdomain of the Sleeping Beauty transposase, 20 mM MES, 650 mM sodium sulfate, 100% D2O

#	Name	Isotope labeling	Concentration
4	MES	natural abundance	20 mM
5	RED subdomain of the Sleeping Beauty transposase	[U-13C; U-15N]	2 mg/mL
6	sodium sulfate	natural abundance	650 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	4.78 ppm	internal	direct	1.0

Referencing offset: 0.36 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	4.78 ppm	internal	direct	1.0

Referencing offset: 0.36 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	4.78 ppm	internal	direct	1.0

Referencing offset: 0.09 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5UNK, Strand ID: A Detail

Release date

2017-05-30

Citation

NMR solution structure of the RED subdomain of the Sleeping Beauty transposase
Konnova, T.A., Singer, C.M., Nesmelova, I.V.
Protein Sci. (2017), 26, 1171-1181, PubMed 28345263 , DOI 10.1002/pro.3167 , Abstract

Related entities 1. Uncharacterized protein, : 12 entities Detail

Experiments performed 6 experiments Detail

1 3D HNCACB

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 293 K, pH 5, Details 2 mg/mL [U-13C; U-15N] RED subdomain of the Sleeping Beauty transposase, 20 mM MES, 650 mM sodium sulfate, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	RED subdomain of the Sleeping Beauty transposase	[U-13C; U-15N]	2 mg/mL
3	sodium sulfate	natural abundance	650 mM

2 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	RED subdomain of the Sleeping Beauty transposase	[U-13C; U-15N]	2 mg/mL
3	sodium sulfate	natural abundance	650 mM

3 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 null, Temperature 293 K, pH 5, Details 2 mg/mL [U-13C; U-15N] RED subdomain of the Sleeping Beauty transposase, 20 mM MES, 650 mM sodium sulfate, 100% D2O

#	Name	Isotope labeling	Concentration
4	MES	natural abundance	20 mM
5	RED subdomain of the Sleeping Beauty transposase	[U-13C; U-15N]	2 mg/mL
6	sodium sulfate	natural abundance	650 mM

4 3D 1H-15N TOCSY

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	RED subdomain of the Sleeping Beauty transposase	[U-13C; U-15N]	2 mg/mL
3	sodium sulfate	natural abundance	650 mM

5 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	MES	natural abundance	20 mM
2	RED subdomain of the Sleeping Beauty transposase	[U-13C; U-15N]	2 mg/mL
3	sodium sulfate	natural abundance	650 mM

6 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
4	MES	natural abundance	20 mM
5	RED subdomain of the Sleeping Beauty transposase	[U-13C; U-15N]	2 mg/mL
6	sodium sulfate	natural abundance	650 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30239_5unk.nef
Input source #2: Coordindates	5unk.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

--------10--------20--------30--------40--------50--------60--
ASMVLSPRDERTLVRKVQINPRTTAKDLVKMLEETGTKVSISTVKRVLYRHNLKGRSARKLE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ASMVLSPRDERTLVRKVQINPRTTAKDLVKMLEETGTKVSISTVKRVLYRHNLKGRSARKLE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	62	0	0	100.0

Content subtype: combined_30239_5unk.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	554		98.4 (chain: A, length: 62)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	581 (1)	noe	98.4 (chain: A, length: 62)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	48 (1)	hbond	58.1 (chain: A, length: 62)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	90 (90)	.	82.3 (chain: A, length: 62)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 328
  - ¹³C chemical shifts: 164
  - ¹⁵N chemical shifts: 62
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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)
57	SER	HG	1.56

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	393	326	83.0
¹³C chemical shifts	287	164	57.1
¹⁵N chemical shifts	71	62	87.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	121	97.6
¹³C chemical shifts	124	56	45.2
¹⁵N chemical shifts	60	59	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	269	205	76.2
¹³C chemical shifts	163	108	66.3
¹⁵N chemical shifts	11	3	27.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	38	88.4
¹³C chemical shifts	43	28	65.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	4	66.7
¹³C chemical shifts	6	2	33.3

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 98.4%
- Total number of restraints: 577
- Weight of restraints: 1.0 (577)
- Potential type of restraints: square-well-parabolic (577)
- Range of distance target values: 2.05, 3.5 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 58.1%
  - Total number of restraints: 48
  - Weight of restraints: 1.0 (48)
  - Potential type of restraints: square-well-parabolic (48)
  - Range of distance target values: 2.25, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: 62, Sequence coverage: 82.3%
- Total number of restraints: 90
- Total number of restraints per polymer type: 90
- Weight of restraints: 1.0 (90)
- Potential type of restraints: square-well-parabolic (90)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA BINDING PROTEIN, dna-binding, helical, helix-turn-helix, transposase

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Found 1 Document (0.498 seconds)

BMRB: 30239

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Uncharacterized protein, : 12 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail