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Found 1 Document (0.831 seconds)

BMRB: 15693

2K27

Solution structure of Human Pax8 Paired Box Domain

Authors

Codutti, L., Esposito, G., Corazza, A., Fogolari, F., Tell, G., Vascotto, C., van Ingen, H., Boelens, R., Viglino, P., Quadrifoglio, F.

Assembly

Pax8 paired Box Domain

Entity

1. Pax8 paired Box Domain (polymer, Thiol state: all free), 159 monomers, 17416.67 Da Detail

MPHNSIRSGH GGLNQLGGAF VNGRPLPEVV RQRIVDLAHQ GVRPCDISRQ LRVSHGCVSK ILGRYYETGS IRPGVIGGSK PKVATPKVVE KIGDYKRQNP TMFAWEIRDR LLAEGVCDND TVPSVSSINR IIRTKVQQPF NLPMDSGAPG GGSHHHHHH

Formula weight

17416.67 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular mechanics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.0 %, Completeness: 83.4 %, Completeness (bb): 88.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.4 % (1506 of 1806)	82.2 % (779 of 948)	82.6 % (575 of 696)	93.8 % (152 of 162)
Backbone	88.4 % (822 of 930)	92.0 % (299 of 325)	83.6 % (383 of 458)	95.2 % (140 of 147)
Sidechain	80.2 % (815 of 1016)	77.0 % (480 of 623)	85.4 % (323 of 378)	80.0 % (12 of 15)
Aromatic	47.2 % (50 of 106)	49.1 % (26 of 53)	44.2 % (23 of 52)	100.0 % (1 of 1)
Methyl	88.9 % (144 of 162)	86.4 % (70 of 81)	91.4 % (74 of 81)

1. Pax8 Paired Box Domain

MPHNSIRSGH GGLNQLGGAF VNGRPLPEVV RQRIVDLAHQ GVRPCDISRQ LRVSHGCVSK ILGRYYETGS IRPGVIGGSK PKVATPKVVE KIGDYKRQNP TMFAWEIRDR LLAEGVCDND TVPSVSSINR IIRTKVQQPF NLPMDSGAPG GGSHHHHHH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.00 (±0.1) K, pH 6.2 (±0.1), Details DTT was added for maintaining Pax8 in reduced state. Oxidation leads to polymerization and precipitation.

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) 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: 0.19 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: 0.19 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: 0.03 ppm, Outliers: 3 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: 0.22 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K27, Strand ID: A Detail

Release date

2008-09-21

Citation

The solution structure of DNA-free Pax-8 paired box domain accounts for redox regulation of transcriptional activity in the pax protein family
Codutti, L., van Ingen, H., Vascotto, C., Fogolari, F., Corazza, A., Tell, G., Quadrifoglio, F., Viglino, P., Boelens, R., Esposito, G.
J. Biol. Chem. (2008), 283, 33321-33328, PubMed 18829450 , DOI 10.1074/jbc.M805717200 , Abstract

Related entities 1. Pax8 paired Box Domain, : 1 : 7 : 98 entities Detail

Interaction partners 1. Pax8 paired Box Domain, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance 2 - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.00 (±0.1) K, pH 6.2 (±0.1), Details DTT was added for maintaining Pax8 in reduced state. Oxidation leads to polymerization and precipitation.

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

2 2D 1H-13C HSQC CT

Instrument

Bruker Avance 2 - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

4 3D C(CO)NH

Instrument

Bruker Avance 2 - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

5 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

6 3D HNCA

Instrument

Bruker Avance 2 - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

7 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

8 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance 2 - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

10 3D 1H-15N NOESY

Instrument

Bruker Avance 2 - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

11 3D 1H-13C NOESY

Instrument

Bruker Avance 2 - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

12 3D CBCANH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

13 3D HN(CO)CACB

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Pax8 Paired Box Domain	[U-100% 13C; U-100% 15N]	0.9 (±0.1) mM
2	DSS	natural abundance	40 (±5.0) uM
3	sodium phosphate	natural abundance	50 (±5.0) mM
4	sodium azide	natural abundance	0.1 (±0.05) %
5	DTT	[U-100% 2H]	15 (±2.0) mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15693_2k27.nef
Input source #2: Coordindates	2k27.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
MPHNSIRSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MPHNSIRSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNP

-------110-------120-------130-------140-------150---------
TMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQPFNLPMDSGAPGGGSHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQPFNLPMDSGAPGGGSHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	159	0	0	100.0

Content subtype: combined_15693_2k27.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1469		93.7 (chain: A, length: 159)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1384 (1)	noe	85.5 (chain: A, length: 159)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1069 (1)	noe	84.3 (chain: A, length: 159)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 93.7%
- Total number of assignments
  - ¹H chemical shifts: 760
  - ¹³C chemical shifts: 558
  - ¹⁵N chemical shifts: 151
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
68	THR	HG1	4.76
85	THR	HG1	4.75
101	THR	HG1	4.72
105	TRP	CD2	127.29
117	CYS	HG	1.91
121	THR	HG1	4.76
134	THR	HG1	4.76

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	948	753	79.4
¹³C chemical shifts	696	557	80.0
¹⁵N chemical shifts	176	151	85.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	325	294	90.5
¹³C chemical shifts	318	241	75.8
¹⁵N chemical shifts	147	139	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	623	459	73.7
¹³C chemical shifts	378	316	83.6
¹⁵N chemical shifts	29	12	41.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	72	85.7
¹³C chemical shifts	84	73	86.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	24	45.3
¹³C chemical shifts	52	22	42.3
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 85.5%
- Total number of restraints: 1369
- Weight of restraints: 1.0 (1369)
- Potential type of restraints: upper-bound-parabolic (1369)
- Range of distance target values: 2.23, 9.04 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 84.3%
  - Total number of restraints: 1066
  - Weight of restraints: 1.0 (1066)
  - Potential type of restraints: lower-bound-parabolic (1066)
  - Range of distance target values: 0.13, 3.22 (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

Keywords 3D NMR, induced fit, NMR, Paired Domain, Pax8, solution structure, triple frequency

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Found 1 Document (0.831 seconds)

BMRB: 15693

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Pax8 paired Box Domain, : 1 : 7 : 98 entities Detail

Interaction partners 1. Pax8 paired Box Domain, : 2 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 4 contents Detail