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BMRB: 4683

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Multiple Modes of Peptide Recognition by the PTB Domain of the cell fate Determinant Numb

Authors

Zwahlen, C., Li, S., Kay, L.E., Pawson, T., Forman-Kay, J.D.

Assembly

dNumb PTB

Entity

1. dNumb PTB (polymer, Thiol state: all free), 171 monomers, 19142.47 Da Detail

GSPGIPDRVP ESSKPHQWQA DEEAVRSATC SFSVKYLGCV EVFESRGMQV CEEALKVLRQ SRRRPVRGLL HVSGDGLRVV DDETKGLIVD QTIEKVSFCA PDRNHERGFS YICRDGTTRR WMCHGFLACK DSGERLSHAV GCAFAVCLER KQRRTRAAAS GFSNMSFEDF P

Formula weight

19142.47 Da

Source organism

melanogaster group

Exptl. method

NMR

Refine. method

TORSION ANGLE DYNAMICS USING ARIA PROTOCOLS FOR AMBIGUOUS RESTRAINTS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 88.4 %, Completeness (bb): 93.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.4 % (1708 of 1933)	91.4 % (924 of 1011)	83.7 % (626 of 748)	90.8 % (158 of 174)
Backbone	93.7 % (948 of 1012)	96.3 % (336 of 349)	92.2 % (460 of 499)	92.7 % (152 of 164)
Sidechain	84.0 % (906 of 1078)	88.8 % (588 of 662)	76.8 % (312 of 406)	60.0 % (6 of 10)
Aromatic	34.7 % (52 of 150)	69.3 % (52 of 75)	0.0 % (0 of 73)	0.0 % (0 of 2)
Methyl	97.4 % (148 of 152)	97.4 % (74 of 76)	97.4 % (74 of 76)

1. dNumb PTB

GSPGIPDRVP ESSKPHQWQA DEEAVRSATC SFSVKYLGCV EVFESRGMQV CEEALKVLRQ SRRRPVRGLL HVSGDGLRVV DDETKGLIVD QTIEKVSFCA PDRNHERGFS YICRDGTTRR WMCHGFLACK DSGERLSHAV GCAFAVCLER KQRRTRAAAS GFSNMSFEDF P

Show sample condition

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type
¹H	H2O	protons	4.75 ppm	internal	direct
¹⁵N	urea	nitrogen	78.98 ppm	null	direct
¹³C	acetate	methyl carbons	25.85 ppm	null	direct

Referencing offset: 0.05 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type
¹H	H2O	protons	4.75 ppm	internal	direct
¹⁵N	urea	nitrogen	78.98 ppm	null	direct
¹³C	acetate	methyl carbons	25.85 ppm	null	direct

Referencing offset: 0.05 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type
¹H	H2O	protons	4.75 ppm	internal	direct
¹⁵N	urea	nitrogen	78.98 ppm	null	direct
¹³C	acetate	methyl carbons	25.85 ppm	null	direct

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type
¹H	H2O	protons	4.75 ppm	internal	direct
¹⁵N	urea	nitrogen	78.98 ppm	null	direct
¹³C	acetate	methyl carbons	25.85 ppm	null	direct

Referencing offset: 0.11 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 1DDM, Strand ID: A, B Detail

Release date

2000-06-18

Citation 1

Multiple modes of peptide recognition by the PTB domain of the cell fate determinant Numb
Zwahlen, C., Li, S., Kay, L.E., Pawson, T., Forman-Kay, J.D.
EMBO J. (2000), 19, 1505-1515, PubMed 10747019 , DOI 10.1093/emboj/19.7.1505 , Abstract

Show more 1 citaion

Citation 2

NMRPipe: a multidimensional spectral processing system based on UNIX pipes
Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.
J. Biomol. NMR (1995), 6, 277-293, PubMed 8520220 , Abstract

Hide non-primary 1 citaion

Related entities 1. dNumb PTB, : 1 : 2 : 83 entities Detail

Interaction partners 1. dNumb PTB, : 10 interactors Detail

More details for 10 interactors identified by 3 citations

Experiments performed 9 experiments Detail

1 1H-15N NOESY

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

2 1H-13C NOESY

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

3 HNCA

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

4 HNCACB

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

5 CBCACONNH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

6 HBCBCACONNH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

7 CCC-TOCSY-CONNH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

8 HCC-TOCSY-CONNH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

9 HCCH-TOCSY

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (500 MHz)

Sample #1

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	dNumb PTB	[U-95% 13C; U-95% 15N]		1.2 mM

Sample #2

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	dNumb PTB	[U-95% 15N]		1.2 mM

Sample #3

Temperature 303 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Type	Concentration
3	dNumb PTB	[U-10% 13C; U-90% 15N]		1.0 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr4683_3.str
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

Content subtype: bmr4683_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	1864		98.2 (chain: 1, length: 171)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 171, Sequence coverage: 98.2%
- Total number of assignments
  - ¹³C chemical shifts: 624
  - ¹H chemical shifts: 1079
  - ¹⁵N chemical shifts: 161
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	748	624	83.4
¹H chemical shifts	1011	925	91.5
¹⁵N chemical shifts	193	161	83.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	342	312	91.2
¹H chemical shifts	349	340	97.4
¹⁵N chemical shifts	164	155	94.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	406	312	76.8
¹H chemical shifts	662	585	88.4
¹⁵N chemical shifts	29	6	20.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	79	76	96.2
¹H chemical shifts	79	77	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	73	0	0.0
¹H chemical shifts	75	51	68.0
¹⁵N chemical shifts	2	0	0.0

Keywords PTB domain

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Found 1 Document (1.948 seconds)

BMRB: 4683

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. dNumb PTB, : 1 : 2 : 83 entities Detail

Interaction partners 1. dNumb PTB, : 10 interactors Detail

Experiments performed 9 experiments Detail

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Chemical shift validation 3 contents Detail