BMRBj - BMREntryMaster

Found 1 Document (0.815 seconds)

BMRB: 18297

2LQ7

E2 binding surface on Uba3 beta-grasp domain undergoes a conformational transition

Authors

Elgin, E.SONAY., Peterson, F.C., Volkman, B.F.

Assembly

Uba3

Entity

1. Uba3 (polymer, Thiol state: not present), 97 monomers, 10647.98 Da Detail

GSQLPQNIQF SPSAKLQEVL DYLTNSASLQ MKSPAITATL EGKNRTLYLQ SVTSIEERTR PNLSKTLKEL GLVDGQELAV ADVTTPQTVL FKLHFTS

Formula weight

10647.98 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 85.2 %, Completeness (bb): 90.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.2 % (960 of 1127)	84.2 % (492 of 584)	87.2 % (383 of 439)	81.7 % (85 of 104)
Backbone	90.7 % (519 of 572)	90.2 % (174 of 193)	90.6 % (260 of 287)	92.4 % (85 of 92)
Sidechain	81.2 % (526 of 648)	81.3 % (318 of 391)	84.9 % (208 of 245)	0.0 % (0 of 12)
Aromatic	80.0 % (40 of 50)	100.0 % (25 of 25)	60.0 % (15 of 25)
Methyl	88.5 % (115 of 130)	87.7 % (57 of 65)	89.2 % (58 of 65)

1. Uba3

GSQLPQNIQF SPSAKLQEVL DYLTNSASLQ MKSPAITATL EGKNRTLYLQ SVTSIEERTR PNLSKTLKEL GLVDGQELAV ADVTTPQTVL FKLHFTS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	Uba3	[U-100% 13C; U-100% 15N]	0.4 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	sodium azide	natural abundance	0.02 %
5	sodium azide	natural abundance	90 %
6	sodium azide	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.53 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.53 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.11 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.06 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LQ7, Strand ID: A Detail

Release date

2012-08-28

Citation

E2-binding surface on Uba3 β-grasp domain undergoes a conformational transition
Elgin, E., Sokmen, N., Peterson, F.C., Volkman, B.F., Da, C., Haas, A.L.
Proteins (2012), 80, 2482-2487, PubMed 22821745 , DOI 10.1002/prot.24148 , Abstract

Related entities 1. Uba3, : 1 : 17 : 16 entities Detail

Interaction partners 1. Uba3, : 15 interactors Detail

More details for 15 interactors identified by 9 citations

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18297_2lq7.nef
Input source #2: Coordindates	2lq7.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

--350-------360-------370-------380-------390-------400-------410-------420-------430-------440--
GSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	97	0	0	100.0

Content subtype: combined_18297_2lq7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	934		90.7 (chain: A, length: 97)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1864 (1)	noe	89.7 (chain: A, length: 97)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	156 (156)	.	87.6 (chain: A, length: 97)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 90.7%
- Total number of assignments
  - ¹H chemical shifts: 485
  - ¹³C chemical shifts: 367
  - ¹⁵N chemical shifts: 82
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	584	485	83.0
¹³C chemical shifts	439	367	83.6
¹⁵N chemical shifts	107	82	76.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	193	171	88.6
¹³C chemical shifts	194	168	86.6
¹⁵N chemical shifts	92	82	89.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	391	314	80.3
¹³C chemical shifts	245	199	81.2
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	53	80.3
¹³C chemical shifts	66	53	80.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	25	100.0
¹³C chemical shifts	25	15	60.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 89.7%
- Total number of restraints: 1864
- Weight of restraints: 1.0 (1864)
- Potential type of restraints: upper-bound-parabolic (1864)
- Range of distance target values: 2.49, 8.65 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 87.6%
- Total number of restraints: 156
- Total number of restraints per polymer type: 156
- Weight of restraints: 1.0 (156)
- Potential type of restraints: square-well-parabolic (156)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords beta grasp domain, E1 enzyme, NMR, Uba3

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 (0.815 seconds)

BMRB: 18297

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Uba3, : 1 : 17 : 16 entities Detail

Interaction partners 1. Uba3, : 15 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail