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BMRB: 18920

2M2L

Solution structure of Entamoeba histolytica HP1 chromodomain

Authors

Wiggins, K.R., Ren, X., Khorasanizadeh, S.

Assembly

Entamoeba histolytica HP1 chromodomain

Entity

1. Entamoeba histolytica HP1 chromodomain (polymer, Thiol state: not present), 67 monomers, 8203.994 Da Detail

MHHHHHHEVP QTFEVERIVR KKIVHGNTSY LVKWKNYSSK DNTWETEDDI RTKYGDLVDD FEKNQKK

Formula weight

8203.994 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.5 %, Completeness: 68.6 %, Completeness (bb): 86.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	68.6 % (572 of 834)	63.2 % (277 of 438)	71.1 % (229 of 322)	89.2 % (66 of 74)
Backbone	86.3 % (345 of 400)	85.9 % (116 of 135)	85.4 % (170 of 199)	89.4 % (59 of 66)
Sidechain	56.5 % (282 of 499)	53.1 % (161 of 303)	60.6 % (114 of 188)	87.5 % (7 of 8)
Aromatic	4.2 % (4 of 96)	4.2 % (2 of 48)	0.0 % (0 of 46)	100.0 % (2 of 2)
Methyl	90.7 % (49 of 54)	88.9 % (24 of 27)	92.6 % (25 of 27)

1. entity

MHHHHHHEVP QTFEVERIVR KKIVHGNTSY LVKWKNYSSK DNTWETEDDI RTKYGDLVDD FEKNQKK

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N-labeled

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		25 mM
4	DTT	natural abundance		1 mM
5	D2O	[U-100% 2H]		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N, 13C-labeled

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]		0.0 ~ 0.0 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		25 mM
9	DTT	natural abundance		1 mM
10	D2O	[U-100% 2H]		5 %

LACS Plot; CA

Referencing offset: 0.18 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.18 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.41 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M2L, Strand ID: A Detail

Release date

2014-05-11

Citation

Characterization of putative readers of epigenetic methyl-marks from Entamoeba histolytica
Ali, I., Wiggins, K.R., Ren, X., Sherman, N., Petri, W., Khorasanizadeh, S.
Not known

Related entities 1. Entamoeba histolytica HP1 chromodomain, : 1 : 76 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N-labeled

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		25 mM
4	DTT	natural abundance		1 mM
5	D2O	[U-100% 2H]		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N, 13C-labeled

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]		0.0 ~ 0.0 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		25 mM
9	DTT	natural abundance		1 mM
10	D2O	[U-100% 2H]		5 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N, 13C-labeled

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]		0.0 ~ 0.0 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		25 mM
9	DTT	natural abundance		1 mM
10	D2O	[U-100% 2H]		5 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N, 13C-labeled

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]		0.0 ~ 0.0 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		25 mM
9	DTT	natural abundance		1 mM
10	D2O	[U-100% 2H]		5 %

5 3D HNCO

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N, 13C-labeled

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]		0.0 ~ 0.0 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		25 mM
9	DTT	natural abundance		1 mM
10	D2O	[U-100% 2H]		5 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N, 13C-labeled

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]		0.0 ~ 0.0 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		25 mM
9	DTT	natural abundance		1 mM
10	D2O	[U-100% 2H]		5 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N, 13C-labeled

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]		0.0 ~ 0.0 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		25 mM
9	DTT	natural abundance		1 mM
10	D2O	[U-100% 2H]		5 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0, Details 15N, 13C-labeled

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]		0.0 ~ 0.0 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium chloride	natural abundance		25 mM
9	DTT	natural abundance		1 mM
10	D2O	[U-100% 2H]		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18920_2m2l.nef
Input source #2: Coordindates	2m2l.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-------
MHHHHHHEVPQTFEVERIVRKKIVHGNTSYLVKWKNYSSKDNTWETEDDIRTKYGDLVDDFEKNQKK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHEVPQTFEVERIVRKKIVHGNTSYLVKWKNYSSKDNTWETEDDIRTKYGDLVDDFEKNQKK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	67	0	0	100.0

Content subtype: combined_18920_2m2l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	600		91.0 (chain: A, length: 67)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3075 (1)	noe	91.0 (chain: A, length: 67)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	61 (61)	.	62.7 (chain: A, length: 67)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 91.0%
- Total number of assignments
  - ¹H chemical shifts: 301
  - ¹³C chemical shifts: 234
  - ¹⁵N chemical shifts: 65
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 91.0%
- Total number of restraints: 2957
- Weight of restraints: 1.0 (2957)
- Potential type of restraints: square-well-parabolic (2957)
- Range of distance target values: 1.4, 2.75 (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: 67, Sequence coverage: 62.7%
- Total number of restraints: 61
- Total number of restraints per polymer type: 61
- Weight of restraints: 1.0 (61)
- Potential type of restraints: square-well-parabolic (61)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords chromodomain, Entamoeba histolytica, HP1