BMRBj - BMREntryMaster

Found 1 Document (1.075 seconds)

BMRB: 34037

5LSD

recombinant mouse Nerve Growth Factor

Authors

Paoletti, F., de Chiara, C., Kelly, G., Lamba, D., Cattaneo, A., Pastore, A.

Assembly

Beta-nerve growth factor

Entity

1. Beta-nerve growth factor (polymer), 118 monomers, 13257.85 × 2 Da Detail

SSTHPVFHMG EFSVCDSVSV WVGDKTTATD IKGKEVTVLA EVNINNSVFR QYFFETKCRA SNPVESGCRG IDSKHWNSYC TTTHTFVKAL TTDEKQAAWR FIRIDTACVC VLSRKATR

Total weight

26515.7 Da

Max. entity weight

13257.85 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS15:SG	1:CYS80:SG
2	disulfide	sing	1:CYS58:SG	1:CYS108:SG
3	disulfide	sing	1:CYS68:SG	1:CYS110:SG
4	disulfide	sing	1:CYS15:SG	1:CYS80:SG
5	disulfide	sing	1:CYS58:SG	1:CYS108:SG
6	disulfide	sing	1:CYS68:SG	1:CYS110:SG

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 93.8 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.8 % (1260 of 1344)	91.7 % (630 of 687)	95.3 % (506 of 531)	98.4 % (124 of 126)
Backbone	98.0 % (690 of 704)	97.9 % (234 of 239)	98.0 % (342 of 349)	98.3 % (114 of 116)
Sidechain	90.6 % (682 of 753)	88.4 % (396 of 448)	93.6 % (276 of 295)	100.0 % (10 of 10)
Aromatic	73.9 % (102 of 138)	73.9 % (51 of 69)	72.7 % (48 of 66)	100.0 % (3 of 3)
Methyl	100.0 % (128 of 128)	100.0 % (64 of 64)	100.0 % (64 of 64)

1. entity 1

SSTHPVFHMG EFSVCDSVSV WVGDKTTATD IKGKEVTVLA EVNINNSVFR QYFFETKCRA SNPVESGCRG IDSKHWNSYC TTTHTFVKAL TTDEKQAAWR FIRIDTACVC VLSRKATR

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details 0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM sodium phosphate, 1 mM EDTA, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.725 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.725 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.725 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 7 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.725 ppm	internal	direct	1.0
¹⁵N	water	protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.65 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5LSD, Strand ID: A, B Detail

Release date

2017-06-28

Citation

Conformational Rigidity within Plasticity Promotes Differential Target Recognition of Nerve Growth Factor
Paoletti, F., de Chiara, C., Kelly, G., Covaceuszach, S., Malerba, F., Yan, R., Lamba, D., Cattaneo, A., Pastore, A.
Front. Mol. Biosci. (2016), 3, 83-83, PubMed 28083536 , DOI 10.3389/fmolb.2016.00083 , Abstract

Related entities 1. Beta-nerve growth factor, : 1 : 5 : 4 : 135 entities Detail

Interaction partners 1. Beta-nerve growth factor, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 14 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details 0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM sodium phosphate, 1 mM EDTA, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

2 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

3 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

5 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 0.1 mM [U-99% 13C; U-99% 15N] Nerve Growth Factor, 50 mM sodium phosphate, 1 mM EDTA, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

6 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

8 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

10 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

11 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

12 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

13 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

14 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	1 mM
2	Nerve Growth Factor	[U-99% 13C; U-99% 15N]	0.1 mM
3	sodium phosphate	natural abundance	50 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34037_5lsd.nef
Input source #2: Coordindates	5lsd.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:15:CYS:SG	A:80:CYS:SG	oxidized, CA 54.507, CB 47.589 ppm	oxidized, CA 54.749, CB 43.524 ppm	2.028
A:58:CYS:SG	A:108:CYS:SG	oxidized, CA 54.066, CB 41.368 ppm	oxidized, CA 55.019, CB 41.084 ppm	2.028
A:68:CYS:SG	A:110:CYS:SG	oxidized, CA 54.436, CB 42.458 ppm	oxidized, CA 56.258, CB 42.223 ppm	2.027
B:15:CYS:SG	B:80:CYS:SG	oxidized, CA 54.507, CB 47.589 ppm	oxidized, CA 54.749, CB 43.524 ppm	2.029
B:58:CYS:SG	B:108:CYS:SG	oxidized, CA 54.066, CB 41.368 ppm	oxidized, CA 55.019, CB 41.084 ppm	2.027
B:68:CYS:SG	B:110:CYS:SG	oxidized, CA 54.436, CB 42.458 ppm	oxidized, CA 56.258, CB 42.223 ppm	2.029

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
SSTHPVFHMGEFSVCDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSKHWNSYCTTTHTFVKALTTDEKQAAWR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SSTHPVFHMGEFSVCDSVSVWVGDKTTATDIKGKEVTVLAEVNINNSVFRQYFFETKCRASNPVESGCRGIDSKHWNSYCTTTHTFVKALTTDEKQAAWR

-------110--------
FIRIDTACVCVLSRKATR
||||||||||||||||||
FIRIDTACVCVLSRKATR

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

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

-------110--------
FIRIDTACVCVLSRKATR
||||||||||||||||||
FIRIDTACVCVLSRKATR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	118	0	0	100.0
B	B	118	0	0	100.0

Content subtype: combined_34037_5lsd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	2508		99.2 (chain: A, length: 118), 99.2 (chain: B, length: 118)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	4740 (1)	noe	99.2 (chain: A, length: 118), 99.2 (chain: B, length: 118)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 99.2%
  - Entity_assembly_ID: B, Chain length: 118, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 1254
  - ¹³C chemical shifts: 1008
  - ¹⁵N chemical shifts: 246
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
85	THR	HG1	6.542

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	687	626	91.1
¹³C chemical shifts	531	504	94.9
¹⁵N chemical shifts	133	123	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	239	236	98.7
¹³C chemical shifts	236	228	96.6
¹⁵N chemical shifts	116	113	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	448	390	87.1
¹³C chemical shifts	295	276	93.6
¹⁵N chemical shifts	17	10	58.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	65	100.0
¹³C chemical shifts	65	65	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	51	73.9
¹³C chemical shifts	66	48	72.7
¹⁵N chemical shifts	3	3	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
85	THR	HG1	6.542

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	687	626	91.1
¹³C chemical shifts	531	504	94.9
¹⁵N chemical shifts	133	123	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	239	236	98.7
¹³C chemical shifts	236	228	96.6
¹⁵N chemical shifts	116	113	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	448	390	87.1
¹³C chemical shifts	295	276	93.6
¹⁵N chemical shifts	17	10	58.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	65	100.0
¹³C chemical shifts	65	65	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	51	73.9
¹³C chemical shifts	66	48	72.7
¹⁵N chemical shifts	3	3	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: 118, Sequence coverage: 99.2%
  - Entity_assembly_ID: B, Chain length: 118, Sequence coverage: 99.2%
- Total number of restraints: 4740
- Weight of restraints: 1.0 (4740)
- Potential type of restraints: square-well-parabolic (4740)
- Range of distance target values: 1.42, 7.7 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords NGF, cell cycle, cystin-knot, dimerfit_1, homodimer

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Found 1 Document (1.075 seconds)

BMRB: 34037

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Beta-nerve growth factor, : 1 : 5 : 4 : 135 entities Detail

Interaction partners 1. Beta-nerve growth factor, : 4 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 3 contents Detail