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BMRB: 19163

2M6Y

The solution structure of the J-domain of human DnaJA1

Authors

Stark, J.L., Mehla, K., Chaika, N., Acton, T.B., Xiao, R., Singh, P.K., Montelione, G.T., Powers, R.

Assembly

J-domain of human DnaJA1

Entity

1. J-domain of human DnaJA1 (polymer, Thiol state: not present), 77 monomers, 9073.118 Da Detail

MGHHHHHHSH MVKETTYYDV LGVKPNATQE ELKKAYRKLA LKYHPDKNPN EGEKFKQISQ AYEVLSDAKK RELYDKG

Formula weight

9073.118 Da

Source organism

Exptl. method

Refine. method

distance geometry, torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.3 %, Completeness: 75.2 %, Completeness (bb): 86.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.2 % (708 of 942)	73.9 % (368 of 498)	76.1 % (277 of 364)	78.8 % (63 of 80)
Backbone	86.0 % (392 of 456)	85.2 % (132 of 155)	86.8 % (197 of 227)	85.1 % (63 of 74)
Sidechain	67.8 % (379 of 559)	68.8 % (236 of 343)	68.1 % (143 of 210)	0.0 % (0 of 6)
Aromatic	4.4 % (4 of 90)	8.9 % (4 of 45)	0.0 % (0 of 45)
Methyl	96.7 % (58 of 60)	100.0 % (30 of 30)	93.3 % (28 of 30)

1. J-domain of DnaJA1

MGHHHHHHSH MVKETTYYDV LGVKPNATQE ELKKAYRKLA LKYHPDKNPN EGEKFKQISQ AYEVLSDAKK RELYDKG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

LACS Plot; CA

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.29 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M6Y, Strand ID: A Detail

Release date

2013-06-23

Citation

Structure and function of human DnaJ homologue subfamily a member 1 (DNAJA1) and its relationship to pancreatic cancer
Stark, J.L., Mehla, K., Chaika, N., Acton, T.B., Xiao, R., Singh, P.K., Montelione, G.T., Powers, R.
Biochemistry (2014), 53, 1360-1372, PubMed 24512202 , DOI 10.1021/bi401329a , Abstract

Related entities 1. J-domain of human DnaJA1, : 1 : 7 : 108 entities Detail

Interaction partners 1. J-domain of human DnaJA1, : 125 interactors Detail

More details for 125 interactors identified by 42 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

3 3D HNCO

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

4 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

5 3D HNCA

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

6 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

8 3D CBCANH

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

9 3D HNHA

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

10 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

11 3D CC(CO)NH

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

12 3D HCC(CO)NH

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

13 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

14 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

15 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz 5 mm, triple-resonance, XYZ-axis gradients TXI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

16 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz 5 mm, triple-resonance, Z-axis gradient cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	J-domain of DnaJA1	[U-13C; U-15N]		1.03 mM
2	MES	natural abundance		20 mM
3	sodium azide	natural abundance		0.02 %
4	DTT	natural abundance		10 mM
5	calcium chloride	natural abundance		5 mM
6	sodium chloride	natural abundance		100 mM
7	DSS	natural abundance		50 uM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19163_2m6y.nef
Input source #2: Coordindates	2m6y.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

--------10--------20--------30--------40--------50--------60--------70-------
MGHHHHHHSHMVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHSHMVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	77	0	0	100.0

Content subtype: combined_19163_2m6y.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	712		87.0 (chain: A, length: 77)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1244 (1)	noe	87.0 (chain: A, length: 77)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	50 (1)	hbond	48.1 (chain: A, length: 77)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	116 (116)	.	81.8 (chain: A, length: 77)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 87.0%
- Total number of assignments
  - ¹H chemical shifts: 372
  - ¹³C chemical shifts: 277
  - ¹⁵N chemical shifts: 63
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 87.0%
- Total number of restraints: 1239
- Weight of restraints: 1.0 (1239)
- Potential type of restraints: square-well-parabolic (1239)
- Range of distance target values: 1.89, 5.83 (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: CNS/XPLOR_distance_constraints_6
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 48.1%
  - Total number of restraints: 50
  - Weight of restraints: 1.0 (50)
  - Potential type of restraints: square-well-parabolic (50)
  - Range of distance target values: 1.9, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 81.8%
- Total number of restraints: 116
- Total number of restraints per polymer type: 116
- Weight of restraints: 1.0 (116)
- Potential type of restraints: square-well-parabolic (116)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords protein