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BMRB: 18480

2LTH

NMR structure of major ampullate spidroin 1 N-terminal domain at pH 5.5

Authors

Otikovs, M., Jaudzems, K., Nordling, K., Landreh, M., Rising, A., Askarieh, G., Knight, S., Johansson, J.

Assembly

major ampullate spidroin 1 N-terminal domain

Entity

1. major ampullate spidroin 1 N-terminal domain (polymer, Thiol state: not present), 137 monomers, 14179.68 × 2 Da Detail

GSGNSHTTPW TNPGLAENFM NSFMQGLSSM PGFTASQLDD MSTIAQSMVQ SIQSLAAQGR TSPNKLQALN MAFASSMAEI AASEEGGGSL STKTSSIASA MSNAFLQTTG VVNQPFINEI TQLVSMFAQA GMNDVSA

Total weight

28359.36 Da

Max. entity weight

14179.68 Da

Source organism

Euprosthenops australis

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 96.7 %, Completeness (bb): 95.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.7 % (1416 of 1465)	97.5 % (730 of 749)	95.2 % (535 of 562)	98.1 % (151 of 154)
Backbone	95.4 % (775 of 812)	97.1 % (272 of 280)	93.5 % (374 of 400)	97.7 % (129 of 132)
Sidechain	98.3 % (766 of 779)	97.7 % (458 of 469)	99.3 % (286 of 288)	100.0 % (22 of 22)
Aromatic	100.0 % (86 of 86)	100.0 % (43 of 43)	100.0 % (42 of 42)	100.0 % (1 of 1)
Methyl	98.5 % (134 of 136)	97.1 % (66 of 68)	100.0 % (68 of 68)

1. Major ampullate spidroin 1

GSGNSHTTPW TNPGLAENFM NSFMQGLSSM PGFTASQLDD MSTIAQSMVQ SIQSLAAQGR TSPNKLQALN MAFASSMAEI AASEEGGGSL STKTSSIASA MSNAFLQTTG VVNQPFINEI TQLVSMFAQA GMNDVSA

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	Major ampullate spidroin 1	[U-99% 13C; U-99% 15N]	1.5 mM
2	D2O	[U-100% 2H]	5 %
3	sodium azide	natural abundance	0.03 %
4	sodium acetate	natural abundance	20 mM
5	sodium chloride	natural abundance	20 mM
6	H2O	natural abundance	95 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.755 ppm	internal	indirect	0.2514495
¹H	water	protons	4.755 ppm	internal	direct	1.0
¹⁵N	water	protons	4.755 ppm	internal	indirect	0.1013291

Referencing offset: -0.41 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.755 ppm	internal	indirect	0.2514495
¹H	water	protons	4.755 ppm	internal	direct	1.0
¹⁵N	water	protons	4.755 ppm	internal	indirect	0.1013291

Referencing offset: -0.41 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.755 ppm	internal	indirect	0.2514495
¹H	water	protons	4.755 ppm	internal	direct	1.0
¹⁵N	water	protons	4.755 ppm	internal	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 4 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.755 ppm	internal	indirect	0.2514495
¹H	water	protons	4.755 ppm	internal	direct	1.0
¹⁵N	water	protons	4.755 ppm	internal	indirect	0.1013291

Referencing offset: -0.35 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-11-25

Citation

Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation
Kronqvist, N., Otikovs, M., Chmyrov, V., Chen, G., Andersson, M., Nordling, K., Landreh, M., Sarr, M., Jornvall, H., Wennmalm, S., Widengren, J., Meng, Q., Rising, A., Otzen, D., Knight, S.D., Jaudzems, K., Johansson, J.
Nat. Commun. (2014), 5, 3254-3254, PubMed 24510122 , DOI 10.1038/ncomms4254 , Abstract

Related entities 1. major ampullate spidroin 1 N-terminal domain, : 1 : 2 : 4 : 3 : 11 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18480_2lth.nef
Input source #2: Coordindates	2lth.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
GSGNSHTTPWTNPGLAENFMNSFMQGLSSMPGFTASQLDDMSTIAQSMVQSIQSLAAQGRTSPNKLQALNMAFASSMAEIAASEEGGGSLSTKTSSIASA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSGNSHTTPWTNPGLAENFMNSFMQGLSSMPGFTASQLDDMSTIAQSMVQSIQSLAAQGRTSPNKLQALNMAFASSMAEIAASEEGGGSLSTKTSSIASA

-------110-------120-------130-------
MSNAFLQTTGVVNQPFINEITQLVSMFAQAGMNDVSA
|||||||||||||||||||||||||||||||||||||
MSNAFLQTTGVVNQPFINEITQLVSMFAQAGMNDVSA

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

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

-------110-------120-------130-------
MSNAFLQTTGVVNQPFINEITQLVSMFAQAGMNDVSA
|||||||||||||||||||||||||||||||||||||
MSNAFLQTTGVVNQPFINEITQLVSMFAQAGMNDVSA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	137	0	0	100.0
B	B	137	0	0	100.0

Content subtype: combined_18480_2lth.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1426		98.5 (chain: A, length: 137)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	5760 (1)	noe	98.5 (chain: A, length: 137), 98.5 (chain: B, length: 137)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 137, Sequence coverage: 98.5%
- Total number of assignments
  - ¹H chemical shifts: 737
  - ¹³C chemical shifts: 537
  - ¹⁵N chemical shifts: 152
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	749	737	98.4
¹³C chemical shifts	562	537	95.6
¹⁵N chemical shifts	155	152	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	280	274	97.9
¹³C chemical shifts	274	251	91.6
¹⁵N chemical shifts	132	129	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	469	463	98.7
¹³C chemical shifts	288	286	99.3
¹⁵N chemical shifts	23	23	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	78	100.0
¹³C chemical shifts	78	78	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	43	100.0
¹³C chemical shifts	42	42	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 137, Sequence coverage: 98.5%
  - Entity_assembly_ID: B, Chain length: 137, Sequence coverage: 98.5%
- Total number of restraints: 5723
- Weight of restraints: 1.0 (5723)
- Potential type of restraints: upper-bound-parabolic (5723)
- Range of distance target values: 2.33, 6.14 (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 STRUCTURAL PROTEIN

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Found 1 Document (0.804 seconds)

BMRB: 18480

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. major ampullate spidroin 1 N-terminal domain, : 1 : 2 : 4 : 3 : 11 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail