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Found 1 Document (3.413 seconds)

BMRB: 11469

2RSD

Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice

Authors

Shindo, H., Tsuchiya, W., Suzuki, R., Yamazaki, T.

Assembly

the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice

Entity

1. the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice, entity 1 (polymer, Thiol state: all other bound), 68 monomers, 7664.665 Da Detail

GSDSFQPEAK VRCICSSTMV NDSMIQCEDQ RCQVWQHLNC VLIPDKPGES AEVPPVFYCE LCRLSRAD

2. ZINC ION (non-polymer), 65.409 × 2 Da

Total weight

7795.483 Da

Max. entity weight

7664.665 Da

Entity Connection

covalent 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	covalent	sing	1:CYS13:SG	2:ZN1:ZN
2	covalent	sing	1:CYS15:SG	2:ZN1:ZN
3	covalent	sing	1:HIS37:ND1	2:ZN1:ZN
4	covalent	sing	1:CYS40:SG	2:ZN1:ZN
5	covalent	sing	1:CYS27:SG	2:ZN1:ZN
6	covalent	sing	1:CYS32:SG	2:ZN1:ZN
7	covalent	sing	1:CYS59:SG	2:ZN1:ZN
8	covalent	sing	1:CYS62:SG	2:ZN1:ZN

Source organism

Oryza sativa Japonica Group

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.9 %, Completeness (bb): 98.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.9 % (753 of 769)	98.3 % (396 of 403)	97.6 % (288 of 295)	97.2 % (69 of 71)
Backbone	98.5 % (392 of 398)	97.7 % (130 of 133)	99.5 % (201 of 202)	96.8 % (61 of 63)
Sidechain	97.7 % (427 of 437)	98.5 % (266 of 270)	96.2 % (153 of 159)	100.0 % (8 of 8)
Aromatic	84.1 % (37 of 44)	95.5 % (21 of 22)	71.4 % (15 of 21)	100.0 % (1 of 1)
Methyl	100.0 % (60 of 60)	100.0 % (30 of 30)	100.0 % (30 of 30)

1. entity 1

GSDSFQPEAK VRCICSSTMV NDSMIQCEDQ RCQVWQHLNC VLIPDKPGES AEVPPVFYCE LCRLSRAD

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
2	ZINC ION	natural abundance		1.0 ~ 2.0 mM
3	sodium chloride	natural abundance		100 mM
4	potassium phosphate	natural abundance		10 mM
5	DTT	natural abundance		5 mM
6	D2O		solvent	100 %

Sample #2

Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
8	ZINC ION	natural abundance		1.0 ~ 2.0 mM
9	sodium chloride	natural abundance		100 mM
10	potassium phosphate	natural abundance		10 mM
11	DTT	natural abundance		5 mM
12	H2O		solvent	92 %
13	D2O		solvent	8 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	external	direct	1.0
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	ammonium hydroxide	nitrogen	external	direct	1.0

Referencing offset: 0.2 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	external	direct	1.0
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	ammonium hydroxide	nitrogen	external	direct	1.0

Referencing offset: 0.2 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	external	direct	1.0
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	ammonium hydroxide	nitrogen	external	direct	1.0

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	TSP	methyl carbons	external	direct	1.0
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	ammonium hydroxide	nitrogen	external	direct	1.0

Referencing offset: 0.72 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2012-08-12

Citation

PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2
Shindo, H., Suzuki, R., Tsuchiya, W., Taichi, M., Nishiuchi, Y., Yamazaki, T.
FEBS Lett. (2012), 586, 1783-1789, PubMed 22626555 , DOI 10.1016/j.febslet.2012.04.063 , Abstract

Related entities 1. the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice, entity 1, : 1 : 2 : 84 entities Detail

Interaction partners 1. the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice, entity 1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
8	ZINC ION	natural abundance		1.0 ~ 2.0 mM
9	sodium chloride	natural abundance		100 mM
10	potassium phosphate	natural abundance		10 mM
11	DTT	natural abundance		5 mM
12	H2O		solvent	92 %
13	D2O		solvent	8 %

2 2D 1H-13C HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
2	ZINC ION	natural abundance		1.0 ~ 2.0 mM
3	sodium chloride	natural abundance		100 mM
4	potassium phosphate	natural abundance		10 mM
5	DTT	natural abundance		5 mM
6	D2O		solvent	100 %

3 3D CBCA(CO)NH

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
8	ZINC ION	natural abundance		1.0 ~ 2.0 mM
9	sodium chloride	natural abundance		100 mM
10	potassium phosphate	natural abundance		10 mM
11	DTT	natural abundance		5 mM
12	H2O		solvent	92 %
13	D2O		solvent	8 %

4 3D HNCO

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
8	ZINC ION	natural abundance		1.0 ~ 2.0 mM
9	sodium chloride	natural abundance		100 mM
10	potassium phosphate	natural abundance		10 mM
11	DTT	natural abundance		5 mM
12	H2O		solvent	92 %
13	D2O		solvent	8 %

5 3D HNCA

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
8	ZINC ION	natural abundance		1.0 ~ 2.0 mM
9	sodium chloride	natural abundance		100 mM
10	potassium phosphate	natural abundance		10 mM
11	DTT	natural abundance		5 mM
12	H2O		solvent	92 %
13	D2O		solvent	8 %

6 3D HCABGCO

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
2	ZINC ION	natural abundance		1.0 ~ 2.0 mM
3	sodium chloride	natural abundance		100 mM
4	potassium phosphate	natural abundance		10 mM
5	DTT	natural abundance		5 mM
6	D2O		solvent	100 %

7 3D HCCH-COSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
2	ZINC ION	natural abundance		1.0 ~ 2.0 mM
3	sodium chloride	natural abundance		100 mM
4	potassium phosphate	natural abundance		10 mM
5	DTT	natural abundance		5 mM
6	D2O		solvent	100 %

8 3D 15N-separated NOESY-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
8	ZINC ION	natural abundance		1.0 ~ 2.0 mM
9	sodium chloride	natural abundance		100 mM
10	potassium phosphate	natural abundance		10 mM
11	DTT	natural abundance		5 mM
12	H2O		solvent	92 %
13	D2O		solvent	8 %

9 3D 13C/15N-separated NOESY-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 92% H2O/8% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
8	ZINC ION	natural abundance		1.0 ~ 2.0 mM
9	sodium chloride	natural abundance		100 mM
10	potassium phosphate	natural abundance		10 mM
11	DTT	natural abundance		5 mM
12	H2O		solvent	92 %
13	D2O		solvent	8 %

10 4D 13C/13C-separated NOESY-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	OsSiz1-PHD	[U-13C; U-15N]	protein	0.5 ~ 1.0 mM
2	ZINC ION	natural abundance		1.0 ~ 2.0 mM
3	sodium chloride	natural abundance		100 mM
4	potassium phosphate	natural abundance		10 mM
5	DTT	natural abundance		5 mM
6	D2O		solvent	100 %

nullKeywords E3 SUMO ligase, histone binding, plant homeodomain (PHD)

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Found 1 Document (3.413 seconds)

BMRB: 11469

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice, entity 1, : 1 : 2 : 84 entities Detail

Interaction partners 1. the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice, entity 1, : 1 interactors Detail

Experiments performed 10 experiments Detail

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