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Found 1 Document (1.234 seconds)

BMRB: 25638

2N39

NMR solution structure of a C-terminal domain of the chromodomain helicase DNA-binding protein 1

Authors

Mohanty, B., Silva, A.P.G., Mackay, J.P., Ryan, D.P.

Assembly

C-terminal domain of the chromodomain helicase DNA-binding protein 1

Entity

1. C-terminal domain of the chromodomain helicase DNA-binding protein 1 (polymer, Thiol state: all free), 108 monomers, 12877.74 Da Detail

GPLGSLDQKT FSICKERMRP VKAALKQLDR PEKGLSEREQ LEHTRQCLIK IGDHITECLK EYTNPEQIKQ WRKNLWIFVS KFTEFDARKL HKLYKHAIKK RQESQQNS

Formula weight

12877.74 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, Water refinement

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 90.7 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.7 % (1245 of 1372)	89.5 % (658 of 735)	91.7 % (476 of 519)	94.1 % (111 of 118)
Backbone	98.8 % (632 of 640)	97.7 % (211 of 216)	99.4 % (318 of 320)	99.0 % (103 of 104)
Sidechain	85.8 % (717 of 836)	86.1 % (447 of 519)	86.5 % (262 of 303)	57.1 % (8 of 14)
Aromatic	65.6 % (63 of 96)	77.1 % (37 of 48)	52.2 % (24 of 46)	100.0 % (2 of 2)
Methyl	100.0 % (98 of 98)	100.0 % (49 of 49)	100.0 % (49 of 49)

1. entity

GPLGSLDQKT FSICKERMRP VKAALKQLDR PEKGLSEREQ LEHTRQCLIK IGDHITECLK EYTNPEQIKQ WRKNLWIFVS KFTEFDARKL HKLYKHAIKK RQESQQNS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 440 uM protein (CHD1-C) 20 mM Sodium phosphate pH 6.5 10 mM NaCl 1 mM DTT 0.3 % Sodium Azide 0.3 % DSS 0.1% 1Xprotease inhibitor

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

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: -0.15 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: -0.15 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: 0.0 ppm, Outliers: 1 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: 0.01 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N39, Strand ID: A Detail

Release date

2016-05-30

Citation

(1)H, (13)C and (15)N resonance assignments of a C-terminal domain of human CHD1
Mohanty, B., Silva, A.P.G., Mackay, J.P., Ryan, D.P.
Biomol. NMR Assign. (2016), 10, 31-34, PubMed 26286320 , DOI 10.1007/s12104-015-9631-1 , Abstract

Related entities 1. C-terminal domain of the chromodomain helicase DNA-binding protein 1, : 1 : 2 : 25 entities Detail

Interaction partners 1. C-terminal domain of the chromodomain helicase DNA-binding protein 1, : 17 interactors Detail

More details for 17 interactors identified by 5 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 440 uM protein (CHD1-C) 20 mM Sodium phosphate pH 6.5 10 mM NaCl 1 mM DTT 0.3 % Sodium Azide 0.3 % DSS 0.1% 1Xprotease inhibitor

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

3 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

7 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

8 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

9 3D HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

12 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CHD1-C	[U-98% 13C; U-98% 15N]	440 uM
2	Sodium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	10 mM
4	DTT	natural abundance	1 mM
5	Sodium Azide	natural abundance	0.3 %
6	DSS	natural abundance	0.3 %
7	1X protease inhibitor	natural abundance	0.1 %
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25638_2n39.nef
Input source #2: Coordindates	2n39.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--------80--------90-------100
GPLGSLDQKTFSICKERMRPVKAALKQLDRPEKGLSEREQLEHTRQCLIKIGDHITECLKEYTNPEQIKQWRKNLWIFVSKFTEFDARKLHKLYKHAIKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSLDQKTFSICKERMRPVKAALKQLDRPEKGLSEREQLEHTRQCLIKIGDHITECLKEYTNPEQIKQWRKNLWIFVSKFTEFDARKLHKLYKHAIKK

--------
RQESQQNS
||||||||
RQESQQNS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_25638_2n39.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1225		99.1 (chain: A, length: 108)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1561 (1)	noe	97.2 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 647
  - ¹³C chemical shifts: 467
  - ¹⁵N chemical shifts: 111
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	735	647	88.0
¹³C chemical shifts	519	467	90.0
¹⁵N chemical shifts	126	111	88.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	216	213	98.6
¹³C chemical shifts	216	214	99.1
¹⁵N chemical shifts	104	103	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	519	434	83.6
¹³C chemical shifts	303	253	83.5
¹⁵N chemical shifts	22	8	36.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	50	100.0
¹³C chemical shifts	50	50	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	37	77.1
¹³C chemical shifts	46	20	43.5
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 97.2%
- Total number of restraints: 1561
- Weight of restraints: 1.0 (1561)
- Potential type of restraints: upper-bound-parabolic (1561)
- Range of distance target values: 2.6, 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

Keywords C-terminal domain, CHD1, chromatin remodelling, nucleosomes

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Found 1 Document (1.234 seconds)

BMRB: 25638

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. C-terminal domain of the chromodomain helicase DNA-binding protein 1, : 1 : 2 : 25 entities Detail

Interaction partners 1. C-terminal domain of the chromodomain helicase DNA-binding protein 1, : 17 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 3 contents Detail