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BMRB: 19340

2MAB

Untangling the Solution Structure of C-Terminal Domain of AciniformSpidroin

Authors

Wang, S., Yang, D.

Assembly

C-Terminal Domain of AciniformSpidroin

Entity

1. C-Terminal Domain of AciniformSpidroin (polymer, Thiol state: not present), 109 monomers, 10880.15 × 2 Da Detail

PSFGLVLNSP NGLRSPQAKA RINNLASALS TAVGRNGVDV NAFTSGLRAT LSNLGDSGMS PNEAKVEVLL EALTAALQLL SSSTLGAVDT TSIGLTSNSV SKAVAQALA

Total weight

21760.3 Da

Max. entity weight

10880.15 Da

Source organism

Trichonephila antipodiana

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.7 %, Completeness (bb): 83.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.7 % (1020 of 1137)	98.3 % (566 of 576)	75.9 % (337 of 444)	100.0 % (117 of 117)
Backbone	83.6 % (540 of 646)	97.8 % (218 of 223)	68.2 % (217 of 318)	100.0 % (105 of 105)
Sidechain	98.0 % (579 of 591)	98.6 % (348 of 353)	96.9 % (219 of 226)	100.0 % (12 of 12)
Aromatic	80.0 % (16 of 20)	100.0 % (10 of 10)	60.0 % (6 of 10)
Methyl	97.5 % (156 of 160)	97.5 % (78 of 80)	97.5 % (78 of 80)

1. entity

PSFGLVLNSP NGLRSPQAKA RINNLASALS TAVGRNGVDV NAFTSGLRAT LSNLGDSGMS PNEAKVEVLL EALTAALQLL SSSTLGAVDT TSIGLTSNSV SKAVAQALA

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CTDtrQA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.01 %
4	D2O	natural abundance		5 %
5	H2O	natural abundance		95 %

LACS Plot; CA

Referencing offset: -0.48 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.48 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-02-12

Citation

Structure and function of C-terminal domain of aciniform spidroin
Wang, S., Huang, W., Yang, D.
Biomacromolecules (2014), 15, 468-477, PubMed 24422432 , DOI 10.1021/bm401709v , Abstract

Related entities 1. C-Terminal Domain of AciniformSpidroin, : 1 : 1 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CTDtrQA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.01 %
4	D2O	natural abundance		5 %
5	H2O	natural abundance		95 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CTDtrQA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.01 %
4	D2O	natural abundance		5 %
5	H2O	natural abundance		95 %

3 3D MQ-(H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CTDtrQA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.01 %
4	D2O	natural abundance		5 %
5	H2O	natural abundance		95 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CTDtrQA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.01 %
4	D2O	natural abundance		5 %
5	H2O	natural abundance		95 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CTDtrQA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.01 %
4	D2O	natural abundance		5 %
5	H2O	natural abundance		95 %

6 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CTDtrQA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.01 %
4	D2O	natural abundance		5 %
5	H2O	natural abundance		95 %

7 3D 13C,15N-filtered NOESY

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
6	CTDtrQA	natural abundance		1 mM
7	CTDtrQA	[U-100% 13C; U-100% 15N]		1 mM
8	sodium phosphate	natural abundance		10 mM
9	D2O	natural abundance		5 %
10	H2O	natural abundance		95 %

8 4D NOESY

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	CTDtrQA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.01 %
4	D2O	natural abundance		5 %
5	H2O	natural abundance		95 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19340_2mab.nef
Input source #2: Coordindates	2mab.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
PSFGLVLNSPNGLRSPQAKARINNLASALSTAVGRNGVDVNAFTSGLRATLSNLGDSGMSPNEAKVEVLLEALTAALQLLSSSTLGAVDTTSIGLTSNSV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PSFGLVLNSPNGLRSPQAKARINNLASALSTAVGRNGVDVNAFTSGLRATLSNLGDSGMSPNEAKVEVLLEALTAALQLLSSSTLGAVDTTSIGLTSNSV

---------
SKAVAQALA
|||||||||
SKAVAQALA

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

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

---------
SKAVAQALA
|||||||||
SKAVAQALA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	109	0	0	100.0
B	B	109	0	0	100.0

Content subtype: combined_19340_2mab.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1026		100.0 (chain: A, length: 109)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	6694 (1)	noe	100.0 (chain: A, length: 109), 100.0 (chain: B, length: 109)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	3346 (1)	noe	100.0 (chain: A, length: 109)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	294 (294)	.	84.4 (chain: A, length: 109), 84.4 (chain: B, length: 109)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	146 (146)	.	84.4 (chain: A, length: 109)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 575
  - ¹³C chemical shifts: 330
  - ¹⁵N chemical shifts: 121
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 109, Sequence coverage: 100.0%
- Total number of restraints: 6677
- Weight of restraints: 1.0 (6677)
- Potential type of restraints: upper-bound-parabolic (6677)
- Range of distance target values: 2.8, 5.4 (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
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 100.0%
  - Total number of restraints: 3340
  - Weight of restraints: 1.0 (3340)
  - Potential type of restraints: upper-bound-parabolic (3340)
  - Range of distance target values: 2.8, 5.4 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - 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: 109, Sequence coverage: 84.4%
  - Entity_assembly_ID: B, Chain length: 109, Sequence coverage: 84.4%
- Total number of restraints: 294
- Total number of restraints per polymer type: 294
- Weight of restraints: 1.0 (294)
- Potential type of restraints: square-well-parabolic (294)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Saveframe: DYANA/DIANA_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 84.4%
  - Total number of restraints: 146
  - Total number of restraints per polymer type: 146
  - Weight of restraints: 1.0 (146)
  - Potential type of restraints: square-well-parabolic (146)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords aciniform spidroin, C-terminal domain, spider silk protein