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BMRB: 18726

2LYI

Repetitive domain (RP) of aciniform spidroin 1 from Nephila antipodiana

Authors

Wang, S., Huang, W., Yang, D.

Assembly

AcSp1-RP

Entity

1. AcSp1-RP (polymer, Thiol state: not present), 167 monomers, 17060.08 Da Detail

MHHHHHHSGS LGDQLTSTLA SALTKTNTLK AVSASKPSAN VAVAIVTSGL KKALGALRIN AGVSSQLTSA VSQAVANVRP GSSPAVYAKA IAAPSVQILV SSGSVNNNNA KQVASTLSEN LVREMANTAR RYRVNVPEAS VQADVSLVTS MTSTFVISSQ TSVQMGG

Formula weight

17060.08 Da

Source organism

Trichonephila antipodiana

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 84.7 %, Completeness (bb): 80.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.7 % (1494 of 1763)	92.4 % (826 of 894)	72.8 % (501 of 688)	92.3 % (167 of 181)
Backbone	80.0 % (794 of 992)	93.8 % (317 of 338)	66.1 % (325 of 492)	93.8 % (152 of 162)
Sidechain	90.9 % (844 of 929)	90.8 % (505 of 556)	92.1 % (326 of 354)	68.4 % (13 of 19)
Aromatic	40.0 % (20 of 50)	52.0 % (13 of 25)	28.0 % (7 of 25)
Methyl	98.7 % (227 of 230)	97.4 % (112 of 115)	100.0 % (115 of 115)

1. AcSp1-RP

MHHHHHHSGS LGDQLTSTLA SALTKTNTLK AVSASKPSAN VAVAIVTSGL KKALGALRIN AGVSSQLTSA VSQAVANVRP GSSPAVYAKA IAAPSVQILV SSGSVNNNNA KQVASTLSEN LVREMANTAR RYRVNVPEAS VQADVSLVTS MTSTFVISSQ TSVQMGG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	AcSp1-RP	[U-100% 13C; U-100% 15N]	2 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	direct	0.25
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1

Referencing offset: -0.32 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	direct	0.25
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1

Referencing offset: -0.32 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	direct	0.25
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1

Referencing offset: 0.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LYI, Strand ID: A Detail

Release date

2013-01-14

Citation

NMR structure note: repetitive domain of aciniform spidroin 1 from Nephila antipodiana
Wang, S., Huang, W., Yang, D.
J. Biomol. NMR (2012), 54, 415-420, PubMed 23129012 , DOI 10.1007/s10858-012-9679-5 , Abstract

Related entities 1. AcSp1-RP, : 1 entities Detail

Experiments performed 7 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18726_2lyi.nef
Input source #2: Coordindates	2lyi.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---
MHHHHHHSGSLGDQLTSTLASALTKTNTLKAVSASKPSANVAVAIVTSGLKKALGALRINAGVSSQLTSAVSQAVANVRPGSSPAVYAKAIAAPSVQILV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHSGSLGDQLTSTLASALTKTNTLKAVSASKPSANVAVAIVTSGLKKALGALRINAGVSSQLTSAVSQAVANVRPGSSPAVYAKAIAAPSVQILV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----100-------110-------120-------130-------140-------150-------160
SSGSVNNNNAKQVASTLSENLVREMANTARRYRVNVPEASVQADVSLVTSMTSTFVISSQTSVQMGG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SSGSVNNNNAKQVASTLSENLVREMANTARRYRVNVPEASVQADVSLVTSMTSTFVISSQTSVQMGG
-------110-------120-------130-------140-------150-------160-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	167	0	0	100.0

Content subtype: combined_18726_2lyi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1484		96.4 (chain: A, length: 167)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3859 (1)	noe	95.2 (chain: A, length: 167)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	186 (186)	.	74.3 (chain: A, length: 167)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 96.4%
- Total number of assignments
  - ¹H chemical shifts: 832
  - ¹³C chemical shifts: 487
  - ¹⁵N chemical shifts: 165
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	894	832	93.1
¹³C chemical shifts	688	487	70.8
¹⁵N chemical shifts	187	165	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	338	318	94.1
¹³C chemical shifts	334	160	47.9
¹⁵N chemical shifts	162	151	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	556	514	92.4
¹³C chemical shifts	354	327	92.4
¹⁵N chemical shifts	25	14	56.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	119	119	100.0
¹³C chemical shifts	119	119	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	13	52.0
¹³C chemical shifts	25	7	28.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 95.2%
- Total number of restraints: 3849
- Weight of restraints: 1.0 (3849)
- Potential type of restraints: upper-bound-parabolic (3849)
- Range of distance target values: 3.4, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 167, Sequence coverage: 74.3%
- Total number of restraints: 186
- Total number of restraints per polymer type: 186
- Weight of restraints: 1.0 (186)
- Potential type of restraints: square-well-parabolic (186)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.53 seconds)

BMRB: 18726

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. AcSp1-RP, : 1 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

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NMR combined restraints 4 contents Detail