BMRBj - BMREntryMaster

Found 1 Document (0.621 seconds)

BMRB: 34351

6QF8

Solution NMR ensemble for human ubiquitin 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), 79 monomers, 8824.056 Da Detail

AMGMQIFVKT LTGKTITLEV EPSDTIENVK AKIQDKEGIP PDQQRLIFAG KQLEDGRTLS DYNIQKESTL HLVLRLRGG

Formula weight

8824.056 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

R-factor based frame picking

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 73.5 %, Completeness (bb): 95.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.5 % (687 of 935)	56.0 % (275 of 491)	91.7 % (330 of 360)	97.6 % (82 of 84)
Backbone	95.1 % (445 of 468)	93.8 % (152 of 162)	95.2 % (219 of 230)	97.4 % (74 of 76)
Sidechain	58.1 % (313 of 539)	37.4 % (123 of 329)	90.1 % (182 of 202)	100.0 % (8 of 8)
Aromatic	0.0 % (0 of 32)	0.0 % (0 of 16)	0.0 % (0 of 16)
Methyl	99.0 % (99 of 100)	98.0 % (49 of 50)	100.0 % (50 of 50)

1. entity 1

AMGMQIFVKT LTGKTITLEV EPSDTIENVK AKIQDKEGIP PDQQRLIFAG KQLEDGRTLS DYNIQKESTL HLVLRLRGG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 1.0 mM [U-99% 13C; U-99% 15N] human ubiquitin, 40 mM sodium phosphate, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	human ubiquitin	[U-99% 13C; U-99% 15N]		1.0 mM
2	sodium phosphate	natural abundance		40 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: 0.03 ppm, Outliers: 1 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: 0.03 ppm, Outliers: 1 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: 0.01 ppm, Outliers: 3 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: 0.22 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6QF8, 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 : 6 : 362 : 333 entities Detail

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

More details for 1 interactors identified by 1 citations

Experiments performed 2 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34351_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: bmr34351_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	728		96.2 (chain: 1, length: 79)
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: 79, Sequence coverage: 96.2%
- Total number of assignments
  - ¹H chemical shifts: 324
  - ¹³C chemical shifts: 325
  - ¹⁵N chemical shifts: 79
- 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 (%)
¹H chemical shifts	491	228	46.4
¹³C chemical shifts	360	325	90.3
¹⁵N chemical shifts	88	79	89.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	162	148	91.4
¹³C chemical shifts	158	144	91.1
¹⁵N chemical shifts	76	71	93.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	329	80	24.3
¹³C chemical shifts	202	181	89.6
¹⁵N chemical shifts	12	8	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	48	92.3
¹³C chemical shifts	52	49	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	0	0.0
¹³C chemical shifts	16	0	0.0

Keywords CoMAND method, R-factor refinement, SIGNALING PROTEIN

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.621 seconds)

BMRB: 34351

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Polyubiquitin-B, : 1 : 6 : 362 : 333 entities Detail

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

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail