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Found 1 Document (0.489 seconds)

BMRB: 30422

6CKU

Solution structure of the zebrafish granulin AaE

Authors

Wang, P., Ni, F.

Assembly

Granulin-A

Entity

1. Granulin-A (polymer), 56 monomers, 5694.396 Da Detail

DVQCGGGFSC HDGETCCPTS QTTWGCCPSP KAVCCDDMQH CCPAGYKCGP GGTCIS

Formula weight

5694.396 Da

Source organism

Danio rerio

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.6 %, Completeness (bb): 99.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	97.6 % (328 of 336)	97.2 % (273 of 281)	100.0 % (55 of 55)
Backbone	99.4 % (166 of 167)	99.1 % (115 of 116)	100.0 % (51 of 51)
Sidechain	95.9 % (162 of 169)	95.8 % (158 of 165)	100.0 % (4 of 4)
Aromatic	80.0 % (16 of 20)	78.9 % (15 of 19)	100.0 % (1 of 1)
Methyl	100.0 % (13 of 13)	100.0 % (13 of 13)

1. entity 1

DVQCGGGFSC HDGETCCPTS QTTWGCCPSP KAVCCDDMQH CCPAGYKCGP GGTCIS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 760 mmHg, Temperature 298 K, pH 6.8, Details 0.5 mM zebrafish granulin AaE, 150 mM sodium chloride and 0.2mM EDTA pH 6.8 90%, H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	zebrafish granulin AaE	natural abundance	0.5 mM
2	sodium chloride	natural abundance	150 mM
3	EDTA	natural abundance	0.2 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 760 mmHg, Temperature 298 K, pH 6.8, Details 0.5 mM [U-15N] zebrafish granulin AaE, 10mM sodium phosphate, 150 mM sodium chloride and 0.2mM EDTA pH 6.8, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	zebrafish granulin AaE	[U-15N]	0.5 mM
5	sodium chloride	natural abundance	150 mM
6	EDTA	natural abundance	0.2 mM

Release date

2018-06-03

Citation

Structure dissection of zebrafish progranulins identifies a well-folded granulin/epithelin module protein with pro-cell survival activities
Wang, P., Chitramuthu, B.K., Bateman, A., Bennett, H.P.J., Xu, P., Ni, F.
Protein Sci. (2018), 27, 1476-1490, PubMed 29732682 , DOI 10.1002/pro.3441 , Abstract

Related entities 1. Granulin-A, : 1 : 1 : 80 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_30422_6cku.nef
Input source #2: Coordindates	6cku.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:4:CYS:SG	A:16:CYS:SG	unknown	unknown	2.029
A:10:CYS:SG	A:26:CYS:SG	unknown	unknown	2.034
A:17:CYS:SG	A:34:CYS:SG	unknown	unknown	2.029
A:27:CYS:SG	A:41:CYS:SG	unknown	unknown	2.026
A:35:CYS:SG	A:48:CYS:SG	unknown	unknown	2.029
A:42:CYS:SG	A:54:CYS:SG	unknown	unknown	2.024

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------
DVQCGGGFSCHDGETCCPTSQTTWGCCPSPKAVCCDDMQHCCPAGYKCGPGGTCIS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DVQCGGGFSCHDGETCCPTSQTTWGCCPSPKAVCCDDMQHCCPAGYKCGPGGTCIS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0

Content subtype: combined_30422_6cku.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	331		100.0 (chain: A, length: 56)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	986 (1)	noe	100.0 (chain: A, length: 56)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	22 (1)	hbond	25.0 (chain: A, length: 56)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	23 (23)	.	66.1 (chain: A, length: 56)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	44 (44)	.	78.6 (chain: A, length: 56)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 276
  - ¹⁵N chemical shifts: 55
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	281	275	97.9
¹⁵N chemical shifts	55	55	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	116	115	99.1
¹⁵N chemical shifts	51	51	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	165	160	97.0
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	13	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	15	78.9
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of restraints: 985
- Weight of restraints: 1.0 (985)
- Potential type of restraints: square-well-parabolic (985)
- Range of distance target values: 3.4, 3.4 (Å)
- Distance restraints per residue
  - Chain_ID: A
- 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: 56, Sequence coverage: 25.0%
  - Total number of restraints: 22
  - Weight of restraints: 1.0 (22)
  - Potential type of restraints: square-well-parabolic (22)
  - Range of distance target values: 1.9, 2.85 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 66.1%
- Total number of restraints: 23
- Total number of restraints per polymer type: 23
- Weight of restraints: 1.0 (23)
- Potential type of restraints: square-well-parabolic (23)
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 78.6%
- Total number of restraints: 44
- Potential type of restraints: undefined (44)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords SIGNALING PROTEIN, beta-hairpin stack, granulin/epithelin module, progranulins

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Found 1 Document (0.489 seconds)

BMRB: 30422

Sample #1

Sample #2

Related entities 1. Granulin-A, : 1 : 1 : 80 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail