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BMRB: 19526

2MEM

Solution NMR structure of SLED domain of Scml2

Authors

Assembly

SLED domain of Scml2

Entity

1. SLED domain of Scml2 (polymer, Thiol state: all free), 119 monomers, 13097.76 Da Detail

GSHMMSTVCV YVNKHGNFGP HLDPKRIQQL PDHFGPGPVN VVLRRIVQAC VDCALETKTV FGYLKPDNRG GEVITASFDG ETHSIQLPPV NSASFALRFL ENFCHSLQCD NLLSSQPFS

Formula weight

13097.76 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 90.0 %, Completeness (bb): 95.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.0 % (1227 of 1363)	90.5 % (639 of 706)	88.4 % (472 of 534)	94.3 % (116 of 123)
Backbone	95.3 % (663 of 696)	95.8 % (228 of 238)	94.8 % (330 of 348)	95.5 % (105 of 110)
Sidechain	86.5 % (672 of 777)	87.8 % (411 of 468)	84.5 % (250 of 296)	84.6 % (11 of 13)
Aromatic	33.3 % (40 of 120)	35.0 % (21 of 60)	31.7 % (19 of 60)
Methyl	100.0 % (124 of 124)	100.0 % (62 of 62)	100.0 % (62 of 62)

1. SLED Scml2

GSHMMSTVCV YVNKHGNFGP HLDPKRIQQL PDHFGPGPVN VVLRRIVQAC VDCALETKTV FGYLKPDNRG GEVITASFDG ETHSIQLPPV NSASFALRFL ENFCHSLQCD NLLSSQPFS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.17 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.17 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-04-21

Citation

Solution NMR structure of the DNA-binding domain from Scml2 (sex comb on midleg-like 2)
Bezsonova, I.
J. Biol. Chem. (2014), 289, 15739-15749, PubMed 24727478 , DOI 10.1074/jbc.M113.524009 , Abstract

Related entities 1. SLED domain of Scml2, : 1 : 31 entities Detail

Interaction partners 1. SLED domain of Scml2, : 12 interactors Detail

More details for 12 interactors identified by 5 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

4 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

5 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

6 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

10 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SLED_Scml2	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		250 mM
4	DTT	natural abundance		2 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19526_2mem.nef
Input source #2: Coordindates	2mem.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

350-----360-------370-------380-------390-------400-------410-------420-------430-------440-------45
GSHMMSTVCVYVNKHGNFGPHLDPKRIQQLPDHFGPGPVNVVLRRIVQACVDCALETKTVFGYLKPDNRGGEVITASFDGETHSIQLPPVNSASFALRFL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMMSTVCVYVNKHGNFGPHLDPKRIQQLPDHFGPGPVNVVLRRIVQACVDCALETKTVFGYLKPDNRGGEVITASFDGETHSIQLPPVNSASFALRFL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------460--------
ENFCHSLQCDNLLSSQPFS
|||||||||||||||||||
ENFCHSLQCDNLLSSQPFS
-------110---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	119	0	0	100.0

Content subtype: combined_19526_2mem.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1218		98.3 (chain: A, length: 119)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	4765 (1)	noe	99.2 (chain: A, length: 119)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	174 (174)	.	95.0 (chain: A, length: 119)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 98.3%
- Total number of assignments
  - ¹H chemical shifts: 635
  - ¹³C chemical shifts: 468
  - ¹⁵N chemical shifts: 115
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 99.2%
- Total number of restraints: 4765
- Weight of restraints: 1.0 (4765)
- Potential type of restraints: upper-bound-parabolic (4765)
- Range of distance target values: 2.36, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 95.0%
- Total number of restraints: 174
- Total number of restraints per polymer type: 174
- Weight of restraints: 1.0 (174)
- Potential type of restraints: square-well-parabolic (174)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PcG, PRC1, Scml2