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Found 1 Document (1.282 seconds)

BMRB: 15670

2K16

Solution structure of the free TAF3 PHD domain

Authors

van Ingen, H., van Schaik, F.M.A., Wienk, H., Timmers, M., Boelens, R.

Assembly

TAF3-PHD finger

Entity

1. TAF3 PHD (polymer, Thiol state: all other bound), 75 monomers, 8600.841 Da Detail

GSHMAMAYVI RDEWGNQIWI CPGCNKPDDG SPMIGCDDCD DWYHWPCVGI MAAPPEEMQW FCPKCANKIK KDKKH

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

8731.659 Da

Max. entity weight

8600.841 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.7 %, Completeness (bb): 82.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.7 % (777 of 876)	97.2 % (448 of 461)	76.0 % (256 of 337)	93.6 % (73 of 78)
Backbone	82.3 % (359 of 436)	97.3 % (145 of 149)	68.9 % (151 of 219)	92.6 % (63 of 68)
Sidechain	95.5 % (486 of 509)	97.1 % (303 of 312)	92.5 % (173 of 187)	100.0 % (10 of 10)
Aromatic	89.8 % (88 of 98)	95.9 % (47 of 49)	81.8 % (36 of 44)	100.0 % (5 of 5)
Methyl	100.0 % (42 of 42)	100.0 % (21 of 21)	100.0 % (21 of 21)

1. TAF3 PHD

GSHMAMAYVI RDEWGNQIWI CPGCNKPDDG SPMIGCDDCD DWYHWPCVGI MAAPPEEMQW FCPKCANKIK KDKKH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	TAF3_PHD	[U-13C; U-15N]	150 mM
2	potassium chloride	natural abundance	150 mM
3	potassium phosphate	natural abundance	20 mM
4	ZnCl2	natural abundance	0.01 mM
5	H2O		95 %
6	D2O		5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.751 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.28 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.751 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.28 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.751 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K16, Strand ID: A Detail

Release date

2008-08-21

Citation

Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3
van Ingen, H., van Schaik, F.M.A., Wienk, H., Ballering, J., Rehmann, H., Deschesne, A.C., Kruijzer, J.A.W., Liskamp, R.M.J., Timmers, H., Boelens, R.
Structure (2008), 16, 1245-1256, PubMed 18682226 , DOI 10.1016/j.str.2008.04.015 , Abstract

Related entities 1. TAF3 PHD, : 1 : 1 : 2 : 42 entities Detail

Interaction partners 1. TAF3 PHD, : 6 interactors Detail

More details for 6 interactors identified by 4 citations

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15670_2k16.nef
Input source #2: Coordindates	2k16.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:21:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:24:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:36:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:39:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:44:HIS:ND1	2:2:ZN:ZN	unknown	unknown	n/a
1:47:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:62:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:65:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

850-----860-------870-------880-------890-------900-------910-------920----
GSHMAMAYVIRDEWGNQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKDKKH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMAMAYVIRDEWGNQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKDKKH
--------10--------20--------30--------40--------50--------60--------70-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	75	0	0	100.0

Content subtype: combined_15670_2k16.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	772		100.0 (chain: A, length: 75)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1506 (1)	noe	98.7 (chain: A, length: 75)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	49 (49)	.	60.0 (chain: A, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 452
  - ¹³C chemical shifts: 247
  - ¹⁵N chemical shifts: 73
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
893	HIS	HE2	10.705

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	461	451	97.8
¹³C chemical shifts	337	247	73.3
¹⁵N chemical shifts	79	73	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	146	98.0
¹³C chemical shifts	150	74	49.3
¹⁵N chemical shifts	68	63	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	312	305	97.8
¹³C chemical shifts	187	173	92.5
¹⁵N chemical shifts	11	10	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	22	84.6
¹³C chemical shifts	26	22	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	47	95.9
¹³C chemical shifts	44	36	81.8
¹⁵N chemical shifts	5	5	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 98.7%
- Total number of restraints: 1506
- Weight of restraints: 1.0 (1506)
- Potential type of restraints: square-well-parabolic (1506)
- Range of distance target values: 1.31, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- 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: 75, Sequence coverage: 60.0%
- Total number of restraints: 49
- Total number of restraints per polymer type: 49
- Weight of restraints: 1.0 (49)
- Potential type of restraints: square-well-parabolic (49)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords histone modifications, NMR, PHD, TFIID

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Found 1 Document (1.282 seconds)

BMRB: 15670

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. TAF3 PHD, : 1 : 1 : 2 : 42 entities Detail

Interaction partners 1. TAF3 PHD, : 6 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail