BMRBj - BMREntryMaster

Found 1 Document (1.545 seconds)

BMRB: 34352

6QH2

Solution NMR ensemble for a chimeric KH-S1 domain construct of exosomal polynucleotide phosphrylase at 298K compiled using the CoMAND method

Authors

ElGamacy, M., Truffault, V., Zhu, H., Coles, M.

Assembly

Polyubiquitin-B

Entity

1. Polyubiquitin-B (polymer, Thiol state: not present), 171 monomers, 18369.62 Da Detail

GAMGRGDISE FAPRIHTIKI NPDKIKDVIG KGGSVIRALT EETGTTIEIE DDGTVKIAAT DGEKAKHAIR RIEEITAEIE VGRVYTGKVT RIVDFGAFVA IGGGKEGLVH ISQIADKRVE KVTDYLQMGQ EVPVKVLEVD RQGRIRLSIK EATEQSQPAA APEAPAAEQG E

Formula weight

18369.62 Da

Source organism

Escherichia coli SE11

Exptl. method

solution NMR

Refine. method

R-factor based frame picking

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.1 %, Completeness: 71.0 %, Completeness (bb): 85.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.0 % (1354 of 1907)	58.7 % (582 of 991)	84.5 % (628 of 743)	83.2 % (144 of 173)
Backbone	85.6 % (868 of 1014)	85.6 % (304 of 355)	85.4 % (422 of 494)	86.1 % (142 of 165)
Sidechain	59.5 % (622 of 1045)	43.7 % (278 of 636)	85.3 % (342 of 401)	25.0 % (2 of 8)
Aromatic	13.8 % (8 of 58)	13.8 % (4 of 29)	13.8 % (4 of 29)
Methyl	95.5 % (210 of 220)	95.5 % (105 of 110)	95.5 % (105 of 110)

1. entity 1

GAMGRGDISE FAPRIHTIKI NPDKIKDVIG KGGSVIRALT EETGTTIEIE DDGTVKIAAT DGEKAKHAIR RIEEITAEIE VGRVYTGKVT RIVDFGAFVA IGGGKEGLVH ISQIADKRVE KVTDYLQMGQ EVPVKVLEVD RQGRIRLSIK EATEQSQPAA APEAPAAEQG E

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.4 mM [U-99% 13C; U-99% 15N] KH-S1, 50 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KH-S1	[U-99% 13C; U-99% 15N]	1.6 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	125 mM
4	HOPES buffer	natural abundance	25 mM

LACS Plot; CA

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

Referencing offset: -0.07 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: -0.07 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: -0.13 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.01 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6QH2, Strand ID: A Detail

Release date

2019-09-25

Citation

Mapping Local Conformational Landscapes of Proteins in Solution
ElGamacy, M., Riss, M., Zhu, H., Truffault, V., Coles, M.
Structure (2019), 27, 853-865, PubMed 30930065 , DOI 10.1016/j.str.2019.03.005 , Abstract

Related entities 1. Polyubiquitin-B, : 1 : 14 : 115 entities Detail

Interaction partners 1. Polyubiquitin-B, : 43 interactors Detail

More details for 43 interactors identified by 5 citations

Experiments performed 5 experiments Detail

1 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.4 mM [U-99% 13C; U-99% 15N] KH-S1, 50 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KH-S1	[U-99% 13C; U-99% 15N]	1.6 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	125 mM
4	HOPES buffer	natural abundance	25 mM

2 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	KH-S1	[U-99% 13C; U-99% 15N]	1.6 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	125 mM
4	HOPES buffer	natural abundance	25 mM

3 3D C(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	KH-S1	[U-99% 13C; U-99% 15N]	1.6 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	125 mM
4	HOPES buffer	natural abundance	25 mM

4 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	KH-S1	[U-99% 13C; U-99% 15N]	1.6 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	125 mM
4	HOPES buffer	natural abundance	25 mM

5 3D CNH-NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	KH-S1	[U-99% 13C; U-99% 15N]	1.6 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	125 mM
4	HOPES buffer	natural abundance	25 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34352_3.str
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

Content subtype: bmr34352_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1440		83.6 (chain: 1, length: 171)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 171, Sequence coverage: 83.6%
- Total number of assignments
  - ¹³C chemical shifts: 599
  - ¹H chemical shifts: 708
  - ¹⁵N chemical shifts: 133
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	743	599	80.6
¹H chemical shifts	991	506	51.1
¹⁵N chemical shifts	184	133	72.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	342	269	78.7
¹H chemical shifts	355	282	79.4
¹⁵N chemical shifts	165	131	79.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	401	330	82.3
¹H chemical shifts	636	224	35.2
¹⁵N chemical shifts	19	2	10.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	112	102	91.1
¹H chemical shifts	112	101	90.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	29	4	13.8
¹H chemical shifts	29	4	13.8

Keywords CoMAND method, PHOSPHATASE, R-factor refinement, SIGNALING PROTEIN

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Found 1 Document (1.545 seconds)

BMRB: 34352

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Polyubiquitin-B, : 1 : 14 : 115 entities Detail

Interaction partners 1. Polyubiquitin-B, : 43 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail