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BMRB: 25382

2MX2

UBX-L domain of VCIP135

Authors

Iwazu, T., Murayama, S., Igarashi, R., Hrioaki, H., Shirakawa, M., Tochio, H.

Assembly

UBX-L domain of VCIP135

Entity

1. UBX-L domain of VCIP135 (polymer), 86 monomers, 9802.160 Da Detail

GSDHSKEKKI RITTNDGRQS MVTLKSSTTF FELQESIARE FNIPPYLQCI RYGFPPKELM PPQAGMEKEP VPLQHGDRIT IEILKG

Formula weight

9802.16 Da

Source organism

Rattus norvegicus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.8 %, Completeness (bb): 83.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.8 % (954 of 1039)	98.6 % (544 of 552)	82.3 % (331 of 402)	92.9 % (79 of 85)
Backbone	83.4 % (417 of 500)	96.5 % (164 of 170)	71.8 % (181 of 252)	92.3 % (72 of 78)
Sidechain	99.7 % (617 of 619)	99.5 % (380 of 382)	100.0 % (230 of 230)	100.0 % (7 of 7)
Aromatic	100.0 % (64 of 64)	100.0 % (32 of 32)	100.0 % (32 of 32)
Methyl	100.0 % (80 of 80)	100.0 % (40 of 40)	100.0 % (40 of 40)

1. VCIP135 UBX

GSDHSKEKKI RITTNDGRQS MVTLKSSTTF FELQESIARE FNIPPYLQCI RYGFPPKELM PPQAGMEKEP VPLQHGDRIT IEILKG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MX2, Strand ID: A Detail

Release date

2016-07-10

Citation

Structure and interaction mode of the UBX-L domain of VCIP135 determined by solution NMR spectroscopy
Iwazu, T., Murayama, S., Igarashi, R., Hrioaki, H., Shirakawa, M., Tochio, H.
Sci. Rep.

Related entities 1. UBX-L domain of VCIP135, : 1 : 6 : 17 entities Detail

Interaction partners 1. UBX-L domain of VCIP135, : 16 interactors Detail

More details for 16 interactors identified by 7 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HN(CO)CA

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D 1H-13C NOESY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

9 3D HCCH-COSY

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

10 2D 1H-13C HSQC

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

11 2D 1H-13C HSQC aliphatic

Instrument

Bruker DRX - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	VCIP135 UBX	[U-13C; U-15N]		1.86 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25382_2mx2.nef
Input source #2: Coordindates	2mx2.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	Error

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--------70--------80------
KEKKIRITTNDGRQSMVTLKSSTTFFELQESIAREFNIPPYLQCIRYGFPPKELMPPQAGMEKEPVPLQHGDRITIEILKG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KEKKIRITTNDGRQSMVTLKSSTTFFELQESIAREFNIPPYLQCIRYGFPPKELMPPQAGMEKEPVPLQHGDRITIEILKG
--------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	81	0	0	100.0

Content subtype: combined_25382_2mx2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	927		No information
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	4584 (1)	noe	100.0 (chain: A, length: 81)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	16 (1)	hbond	9.9 (chain: A, length: 81)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	92 (92)	.	86.4 (chain: A, length: 81)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 100.0%
- Total number of restraints: 4584
- Weight of restraints: 1.0 (4584)
- Potential type of restraints: upper-bound-parabolic (4584)
- Range of distance target values: 2.49, 9.59 (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: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 9.9%
  - Total number of restraints: 16
  - Weight of restraints: 1.0 (16)
  - Potential type of restraints: upper-bound-parabolic (16)
  - Range of distance target values: 2.2, 3.3 (Å)
  - Histogram of 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: 81, Sequence coverage: 86.4%
- Total number of restraints: 92
- Total number of restraints per polymer type: 92
- Weight of restraints: 1.0 (92)
- Potential type of restraints: square-well-parabolic (92)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Golgi, UBX domain, mitosis