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BMRB: 18844

2M17

ubiquitin-like domain-containing C-terminal domain phosphatase (UBLCP1)

Authors

Lee, W., Yun, J.

Assembly

UBLCP1

Entity

1. UBLCP1, entity 1 (polymer), 82 monomers, 8982.570 Da Detail

MALPIIVKWG GQEYSVTTLS EDDTVLDLKQ FLKTLTGVLP ERQKLLGLKV KGKPAENDVK LGALKLKPNT KIMMMGTREE SX

2. PL (non-polymer), na Da
3. UBLCP1, entity LL5 (non-polymer), 334.436 × 5 Da
4. ORI (non-polymer), na Da

Total weight

10654.75 Da

Max. entity weight

8982.57 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 84.9 %, Completeness (bb): 85.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.9 % (826 of 973)	91.4 % (467 of 511)	73.9 % (280 of 379)	95.2 % (79 of 83)
Backbone	85.6 % (409 of 478)	97.0 % (160 of 165)	72.9 % (172 of 236)	100.0 % (77 of 77)
Sidechain	86.3 % (491 of 569)	88.7 % (307 of 346)	83.9 % (182 of 217)	33.3 % (2 of 6)
Aromatic	26.7 % (8 of 30)	46.7 % (7 of 15)	0.0 % (0 of 14)	100.0 % (1 of 1)
Methyl	93.5 % (101 of 108)	92.6 % (50 of 54)	94.4 % (51 of 54)

1. entity 1

MALPIIVKWG GQEYSVTTLS EDDTVLDLKQ FLKTLTGVLP ERQKLLGLKV KGKPAENDVK LGALKLKPNT KIMMMGTREE SX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

LACS Plot; CA

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M17, Strand ID: A Detail

Release date

2013-05-29

Citation

Solution structure and Rpn1 interaction of the UBL domain of human RNA polymerase II C-terminal domain phosphatase
Yun, J., Ko, S., Lee, C., Cheong, H., Cheong, C., Yoon, J., Lee, W.
PLoS One (2013), 8, e62981-e62981, PubMed 23667555 , DOI 10.1371/journal.pone.0062981 , Abstract

Related entities 1. UBLCP1, entity 1, : 1 : 7 : 95 entities Detail

Interaction partners 1. UBLCP1, entity 1, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

2 3D HNCA

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

3 3D HNCACB

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

4 3D HNCO

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

5 3D CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

6 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

7 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

8 3D 1H-13C NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

9 3D HBHA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		0.6 mM
2	entity_1	[U-13C; U-15N]		0.6 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18844_2m17.nef
Input source #2: Coordindates	2m17.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:81:SER:C	1:82:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	90	NH2	AMINO GROUP	Coordinates

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------8090
MALPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTREESX
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MALPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTREESX
--------10--------20--------30--------40--------50--------60--------70--------80--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	82	0	0	100.0

Content subtype: combined_18844_2m17.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	798		97.6 (chain: A, length: 82)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2809 (1)	noe	96.3 (chain: A, length: 82)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	100 (100)	.	87.8 (chain: A, length: 82)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 97.6%
- Total number of assignments
  - ¹H chemical shifts: 463
  - ¹³C chemical shifts: 258
  - ¹⁵N chemical shifts: 77
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 96.3%
- Total number of restraints: 2809
- Weight of restraints: 1.0 (2809)
- Potential type of restraints: upper-bound-parabolic (2809)
- Range of distance target values: 2.31, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 87.8%
- Total number of restraints: 100
- Total number of restraints per polymer type: 100
- Weight of restraints: 1.0 (100)
- Potential type of restraints: square-well-parabolic (100)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ubiquitin-like domain-containing C-terminal domain phosphatase (UBLCP1)