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BMRB: 18909

2M2E

Solution NMR structure of the SANT domain of human DNAJC2; Notrheast structural genomics consortium target HR8254a

Authors

Lemak, A., Yee, A., Houliston, S., Garcia, M., Ong, M., Arrowsmith, C.

Assembly

hs00507

Entity

1. hs00507 (polymer, Thiol state: all free), 73 monomers, 8476.797 Da Detail

QGFTPWTTEE QKLLEQALKT YPVNTPERWK KIAEAVPGRT KKDCMKRYKE LVEMVKAKKA AQEQVLNASR AKK

Formula weight

8476.797 Da

Source organism

Exptl. method

Refine. method

restrained molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 92.4 %, Completeness (bb): 92.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.4 % (841 of 910)	89.7 % (436 of 486)	96.2 % (333 of 346)	92.3 % (72 of 78)
Backbone	92.1 % (396 of 430)	85.4 % (123 of 144)	95.4 % (207 of 217)	95.7 % (66 of 69)
Sidechain	93.5 % (515 of 551)	91.5 % (313 of 342)	98.0 % (196 of 200)	66.7 % (6 of 9)
Aromatic	96.0 % (48 of 50)	96.0 % (24 of 25)	95.7 % (22 of 23)	100.0 % (2 of 2)
Methyl	98.6 % (71 of 72)	97.2 % (35 of 36)	100.0 % (36 of 36)

1. entity

QGFTPWTTEE QKLLEQALKT YPVNTPERWK KIAEAVPGRT KKDCMKRYKE LVEMVKAKKA AQEQVLNASR AKK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M2E, Strand ID: A Detail

Release date

2013-02-07

Citation

NMR solution structure of the SANT domain of human DnaJC2
Lemak, A., Yee, A., Houliston, S., Garcia, M., Ong, M., Arrowsmith, C.
Not known

Related entities 1. hs00507, : 1 : 36 entities Detail

Interaction partners 1. hs00507, : 5 interactors Detail

More details for 5 interactors identified by 2 citations

Experiments performed 9 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

2 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

6 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

9 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Type	Concentration
1	hs00507	[U-13C; U-15N]		0.5 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		500 mM
4	ZnSO4	natural abundance		10 uM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.01 %
7	benzamidine	natural abundance		10 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18909_2m2e.nef
Input source #2: Coordindates	2m2e.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

-550-----560-------570-------580-------590-------600-------610-------620-
QGFTPWTTEEQKLLEQALKTYPVNTPERWKKIAEAVPGRTKKDCMKRYKELVEMVKAKKAAQEQVLNASRAKK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QGFTPWTTEEQKLLEQALKTYPVNTPERWKKIAEAVPGRTKKDCMKRYKELVEMVKAKKAAQEQVLNASRAKK
--------10--------20--------30--------40--------50--------60--------70---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0

Content subtype: combined_18909_2m2e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	871		98.6 (chain: A, length: 73)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2160 (1)	noe	97.3 (chain: A, length: 73)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	125 (125)	.	94.5 (chain: A, length: 73)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 465
  - ¹³C chemical shifts: 332
  - ¹⁵N chemical shifts: 74
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: 73, Sequence coverage: 97.3%
- Total number of restraints: 2160
- Weight of restraints: 1.0 (2160)
- Potential type of restraints: square-well-parabolic (2160)
- Range of distance target values: 2.25, 3.9 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 94.5%
- Total number of restraints: 125
- Total number of restraints per polymer type: 125
- Weight of restraints: 1.0 (125)
- Potential type of restraints: square-well-parabolic (125)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA-binding, DNAJC2, NESG, Northeast structural genomics consortium, SANT domain, SGC, Structural Genomics Consortium, transcription regulator