BMRB: 11237

Solution structure of the first and second PHD domain from Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog

Authors

Qin, X., Hayashi, F., Yokoyama, S.

Assembly

Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog

Entity

1. PHD domain (polymer, Thiol state: free and other bound), 111 monomers, 11866.52 Da Detail

GSSGSSGANC AVCDSPGDLL DQFFCTTCGQ HYHGMCLDIA VTPLKRAGWQ CPECKVCQNC KQSGEDSKML VCDTCDKGYH TFCLQPVMKS VPTNGWKCKN CRICISGPSS G

2. ZN (non-polymer), 65.409 × 4 Da

Total weight

12128.155 Da

Max. entity weight

11866.52 Da

Entity Connection

na 16 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS10:SG	2:ZN1:ZN
2	na	sing	1:CYS13:SG	2:ZN1:ZN
3	na	sing	1:CYS25:SG	2:ZN1:ZN
4	na	sing	1:CYS28:SG	2:ZN1:ZN
5	na	sing	1:HIS33:ND1	2:ZN1:ZN
6	na	sing	1:CYS36:SG	2:ZN1:ZN
7	na	sing	1:CYS51:SG	2:ZN1:ZN
8	na	sing	1:CYS54:SG	2:ZN1:ZN
9	na	sing	1:CYS57:SG	2:ZN1:ZN
10	na	sing	1:CYS60:SG	2:ZN1:ZN
11	na	sing	1:CYS72:SG	2:ZN1:ZN
12	na	sing	1:CYS75:SG	2:ZN1:ZN
13	na	sing	1:HIS80:ND1	2:ZN1:ZN
14	na	sing	1:CYS83:SG	2:ZN1:ZN
15	na	sing	1:CYS98:SG	2:ZN1:ZN
16	na	sing	1:CYS101:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 98.5 %, Completeness (bb): 97.9 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	98.5 % (1181 of 1199)	98.4 % (613 of 623)	98.9 % (454 of 459)	97.4 % (114 of 117)
Backbone	97.9 % (640 of 654)	97.4 % (222 of 228)	98.4 % (316 of 321)	97.1 % (102 of 105)
Sidechain	99.2 % (639 of 644)	99.0 % (391 of 395)	99.6 % (236 of 237)	100.0 % (12 of 12)
Aromatic	100.0 % (82 of 82)	100.0 % (41 of 41)	100.0 % (39 of 39)	100.0 % (2 of 2)
Methyl	100.0 % (80 of 80)	100.0 % (40 of 40)	100.0 % (40 of 40)

1. PHD domain

GSSGSSGANC AVCDSPGDLL DQFFCTTCGQ HYHGMCLDIA VTPLKRAGWQ CPECKVCQNC KQSGEDSKML VCDTCDKGYH TFCLQPVMKS VPTNGWKCKN CRICISGPSS G

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 293 (±0.1) K, pH 7.0 (±0.05), Details 0.94mM 13C, 15N-labeled {protein;} 20mM {d-Tris-HCl(pH7.0);} 100mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} 0.05mM ZnCl2+1mM {IDA;} 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PHD domain	[U-13C; U-15N]	protein	0.94 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	ZnCl2	natural abundance	salt	0.05 mM
7	IDA	natural abundance	salt	1 mM
8	H2O		solvent	90 %
9	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.06 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.06 ppm, Outliers: 2 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.27 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

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

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Release date

2011-08-02

Citation

Solution structure of the first and second PHD domain from Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog
Qin, X., Hayashi, F., Yokoyama, S.

Related entities 1. PHD domain, : 1 : 2 : 66 entities Detail

Interaction partners 1. PHD domain, : 23 interactors Detail

Experiments performed 2 experiments Detail