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Found 1 Document (1.304 seconds)

BMRB: 18296

2LQ6

Solution structure of BRD1 PHD2 finger

Authors

Liu, L., Wu, J.

Assembly

BRD1 PHD2 finger

Entity

1. BRD1 PHD2 finger, entity 1 (polymer, Thiol state: free and other bound), 87 monomers, 9638.106 Da Detail

MGHHHHHHMN IPPARWKLTC YLCKQKGVGA SIQCHKANCY TAFHVTCAQK AGLYMKMEPV KELTGGGTTF SVRKTAYCDV HTPPGST

2. ZINC ION (non-polymer, Thiol state: not present), 65.409 × 2 Da

Total weight

9768.925 Da

Max. entity weight

9638.106 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.0 %, Completeness: 81.1 %, Completeness (bb): 87.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.1 % (802 of 989)	84.9 % (434 of 511)	74.6 % (291 of 390)	87.5 % (77 of 88)
Backbone	87.5 % (448 of 512)	87.0 % (154 of 177)	87.7 % (222 of 253)	87.8 % (72 of 82)
Sidechain	76.3 % (424 of 556)	83.8 % (280 of 334)	64.4 % (139 of 216)	83.3 % (5 of 6)
Aromatic	29.0 % (29 of 100)	56.0 % (28 of 50)	0.0 % (0 of 49)	100.0 % (1 of 1)
Methyl	97.4 % (74 of 76)	97.4 % (37 of 38)	97.4 % (37 of 38)

1. entity 1

MGHHHHHHMN IPPARWKLTC YLCKQKGVGA SIQCHKANCY TAFHVTCAQK AGLYMKMEPV KELTGGGTTF SVRKTAYCDV HTPPGST

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BRD1_PHD2_finger	[U-15N]	0.3 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaCl	natural abundance	150 mM
5	Bis-tris methane	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	NaCl	natural abundance	150 mM
10	Bis-tris methane	natural abundance	20 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
12	D2O	natural abundance	100 %
13	NaCl	natural abundance	150 mM
14	Bis-tris methane	natural abundance	20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 4 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 4 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.18 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -1.76 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LQ6, Strand ID: A Detail

Release date

2012-10-21

Citation

Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA
Liu, L., Qin, S., Zhang, J., Ji, P., Shi, Y., Wu, J.
J. Struct. Biol. (2012), 180, 165-173, PubMed 22820306 , DOI 10.1016/j.jsb.2012.06.014 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 17244 released on 2012-07-24
Title Structural basis for histone code recognition by BRPF2-PHD1 finger

Related entities 1. BRD1 PHD2 finger, entity 1, : 1 : 4 : 67 entities Detail

Interaction partners 1. BRD1 PHD2 finger, entity 1, : 16 interactors Detail

More details for 16 interactors identified by 4 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BRD1_PHD2_finger	[U-15N]	0.3 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaCl	natural abundance	150 mM
5	Bis-tris methane	natural abundance	20 mM

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	NaCl	natural abundance	150 mM
10	Bis-tris methane	natural abundance	20 mM

3 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	NaCl	natural abundance	150 mM
10	Bis-tris methane	natural abundance	20 mM

4 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	NaCl	natural abundance	150 mM
10	Bis-tris methane	natural abundance	20 mM

5 3D HN(CO)CA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	NaCl	natural abundance	150 mM
10	Bis-tris methane	natural abundance	20 mM

6 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	NaCl	natural abundance	150 mM
10	Bis-tris methane	natural abundance	20 mM

7 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	NaCl	natural abundance	150 mM
10	Bis-tris methane	natural abundance	20 mM

8 3D HCCH-COSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
12	D2O	natural abundance	100 %
13	NaCl	natural abundance	150 mM
14	Bis-tris methane	natural abundance	20 mM

9 3D HCCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
12	D2O	natural abundance	100 %
13	NaCl	natural abundance	150 mM
14	Bis-tris methane	natural abundance	20 mM

10 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	NaCl	natural abundance	150 mM
10	Bis-tris methane	natural abundance	20 mM

11 3D 1H-13C NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	BRD1_PHD2_finger	[U-13C; U-15N]	0.4 mM
12	D2O	natural abundance	100 %
13	NaCl	natural abundance	150 mM
14	Bis-tris methane	natural abundance	20 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18296_2lq6.nef
Input source #2: Coordindates	2lq6.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)
1:41:THR:OG1	2:2:ZN:ZN	unknown	unknown	n/a
1:22:LEU:O	2:1:ZN:ZN	unknown	unknown	n/a
1:39:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:23:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:78:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:47:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:44:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:81:HIS:ND1	2:2:ZN:ZN	unknown	unknown	n/a
1:34:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:20: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

--310-----320-------330-------340-------350-------360-------370-------380-------390----
MGHHHHHHMNIPPARWKLTCYLCKQKGVGASIQCHKANCYTAFHVTCAQKAGLYMKMEPVKELTGGGTTFSVRKTAYCDVHTPPGST
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHMNIPPARWKLTCYLCKQKGVGASIQCHKANCYTAFHVTCAQKAGLYMKMEPVKELTGGGTTFSVRKTAYCDVHTPPGST
--------10--------20--------30--------40--------50--------60--------70--------80-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0

Content subtype: combined_18296_2lq6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	10		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	807		90.8 (chain: A, length: 87)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1598 (1)	noe	90.8 (chain: A, length: 87)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	12 (1)	undefined	9.2 (chain: A, length: 87)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	36 (1)	hbond	26.4 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 90.8%
- Total number of assignments
  - ¹H chemical shifts: 441
  - ¹³C chemical shifts: 289
  - ¹⁵N chemical shifts: 77
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	511	441	86.3
¹³C chemical shifts	390	289	74.1
¹⁵N chemical shifts	90	77	85.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	177	156	88.1
¹³C chemical shifts	174	152	87.4
¹⁵N chemical shifts	82	72	87.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	334	285	85.3
¹³C chemical shifts	216	137	63.4
¹⁵N chemical shifts	8	5	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	40	95.2
¹³C chemical shifts	42	37	88.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	28	56.0
¹³C chemical shifts	49	0	0.0
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 90.8%
- Total number of restraints: 1589
- Weight of restraints: 1.0 (1589)
- Potential type of restraints: square-well-parabolic (1589)
- Range of distance target values: 1.75, 4.15 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 9.2%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: square-well-parabolic (12)
  - Range of distance target values: 3.55, 3.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 26.4%
    - Total number of restraints: 36
    - Weight of restraints: 1.0 (36)
    - Potential type of restraints: square-well-parabolic (36)
    - Range of distance target values: 2.2, 3.2 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Keywords PHD finger

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Found 1 Document (1.304 seconds)

BMRB: 18296

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. BRD1 PHD2 finger, entity 1, : 1 : 4 : 67 entities Detail

Interaction partners 1. BRD1 PHD2 finger, entity 1, : 16 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail