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Found 1 Document (0.75 seconds)

BMRB: 15989

2K9N

Solution NMR structure of the R2R3 DNA binding domain of Myb1 protein from protozoan parasite Trichomonas vaginalis

Authors

Lou, Y., Wei, S., Rajasekaran, M., Chou, C., Hsu, H., Tai, J., Chen, C.

Assembly

Myb1

Entity

1. Myb1 (polymer, Thiol state: all free), 107 monomers, 13193.04 Da Detail

KVKFTEEEDL KLQQLVMRYG AKDWIRISQL MITRNPRQCR ERWNNYINPA LRTDPWSPEE DMLLDQKYAE YGPKWNKISK FLKNRSDNNI RNRWMMIARH RAKHQKS

Formula weight

13193.04 Da

Source organism

Trichomonas vaginalis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, heteronucl_NOEs

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.6 %, Completeness (bb): 97.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.6 % (1318 of 1378)	95.1 % (704 of 740)	95.9 % (495 of 516)	97.5 % (119 of 122)
Backbone	97.9 % (619 of 632)	97.6 % (206 of 211)	98.4 % (314 of 319)	97.1 % (99 of 102)
Sidechain	94.2 % (802 of 851)	94.1 % (498 of 529)	94.0 % (284 of 302)	100.0 % (20 of 20)
Aromatic	81.7 % (98 of 120)	81.7 % (49 of 60)	80.0 % (44 of 55)	100.0 % (5 of 5)
Methyl	97.6 % (82 of 84)	97.6 % (41 of 42)	97.6 % (41 of 42)

1. R2R3 DNA binding domain

KVKFTEEEDL KLQQLVMRYG AKDWIRISQL MITRNPRQCR ERWNNYINPA LRTDPWSPEE DMLLDQKYAE YGPKWNKISK FLKNRSDNNI RNRWMMIARH RAKHQKS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
6	entity	[U-13C; U-15N]	1 mM
7	sodium chloride	natural abundance	50 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium azide	natural abundance	5 mM
10	beta-mercaptoethanol	natural abundance	20 mM

LACS Plot; CA

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

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.41 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K9N, Strand ID: A Detail

Heteronucl. NOE

92 NOE values in 1 lists
Value type relative intensities, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 K, pH 6.0 Detail

Release date

2009-04-03

Citation

NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis
Lou, Y., Wei, S., Rajasekaran, M., Chou, C., Hsu, H., Tai, J., Chen, C.
Nucleic Acids Res. (2009), 37, 2381-2394, PubMed 19246540 , DOI 10.1093/nar/gkp097 , Abstract

Related entities 1. Myb1, : 1 : 1 : 263 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
6	entity	[U-13C; U-15N]	1 mM
7	sodium chloride	natural abundance	50 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium azide	natural abundance	5 mM
10	beta-mercaptoethanol	natural abundance	20 mM

7 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
6	entity	[U-13C; U-15N]	1 mM
7	sodium chloride	natural abundance	50 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium azide	natural abundance	5 mM
10	beta-mercaptoethanol	natural abundance	20 mM

9 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

10 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

11 2D 1H-15N HxNOE

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	entity	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	20 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15989_2k9n.nef
Input source #2: Coordindates	2k9n.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KVKFTEEEDLKLQQLVMRYGAKDWIRISQLMITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRWMMIARH

-------
RAKHQKS
|||||||
RAKHQKS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	107	0	0	100.0

Content subtype: combined_15989_2k9n.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1319		100.0 (chain: A, length: 107)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1903 (1)	noe	100.0 (chain: A, length: 107)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	28 (1)	hbond	20.6 (chain: A, length: 107)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	138 (138)	.	81.3 (chain: A, length: 107)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 705
  - ¹³C chemical shifts: 493
  - ¹⁵N chemical shifts: 121
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	740	705	95.3
¹³C chemical shifts	516	493	95.5
¹⁵N chemical shifts	134	121	90.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	211	208	98.6
¹³C chemical shifts	214	211	98.6
¹⁵N chemical shifts	102	99	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	529	497	94.0
¹³C chemical shifts	302	282	93.4
¹⁵N chemical shifts	32	22	68.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	42	89.4
¹³C chemical shifts	47	41	87.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	49	81.7
¹³C chemical shifts	55	44	80.0
¹⁵N chemical shifts	5	5	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 100.0%
- Total number of restraints: 1903
- Weight of restraints: 1.0 (1903)
- Potential type of restraints: square-well-parabolic (1903)
- Range of distance target values: 2.3, 4.5 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 20.6%
  - Total number of restraints: 28
  - Weight of restraints: 1.0 (28)
  - Potential type of restraints: square-well-parabolic (28)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 81.3%
- Total number of restraints: 138
- Total number of restraints per polymer type: 138
- Weight of restraints: 1.0 (138)
- Potential type of restraints: square-well-parabolic (138)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords HADDOCK, Myb, NMR, R2R3 DNA binding domain, Trichomonas vaginalis, Myb1, R2R3 Domain

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Found 1 Document (0.75 seconds)

BMRB: 15989

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Myb1, : 1 : 1 : 263 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail