BMRBj - BMREntryMaster

Found 1 Document (1.417 seconds)

BMRB: 30040

5IX9

Cell surface anchoring domain

Authors

Guo, S., Langelaan, D.

Assembly

Antifreeze protein

Entity

1. Antifreeze protein (polymer, Thiol state: not present), 76 monomers, 7823.576 Da Detail

GNAIGFITKL DGSVTVQSIN GQERVLKLGD PIFFGETVLT GGSGSVTIAF VDGTDVVIGG DSIVEMTDEI YNTGDN

Formula weight

7823.576 Da

Source organism

Marinomonas primoryensis

Exptl. method

solution NMR

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.2 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.2 % (766 of 805)	92.3 % (374 of 405)	97.8 % (312 of 319)	98.8 % (80 of 81)
Backbone	96.7 % (439 of 454)	94.5 % (155 of 164)	97.7 % (210 of 215)	98.7 % (74 of 75)
Sidechain	93.5 % (387 of 414)	90.0 % (217 of 241)	98.2 % (164 of 167)	100.0 % (6 of 6)
Aromatic	100.0 % (48 of 48)	100.0 % (24 of 24)	100.0 % (24 of 24)
Methyl	93.3 % (97 of 104)	90.4 % (47 of 52)	96.2 % (50 of 52)

1. Antifreeze protein

GNAIGFITKL DGSVTVQSIN GQERVLKLGD PIFFGETVLT GGSGSVTIAF VDGTDVVIGG DSIVEMTDEI YNTGDN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 20 mM TRIS, 50 mM sodium chloride, 2 mM CaCl2, 2 mM MgCl2, 3 mM 13C MpAFP_RINM, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

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	4.78 ppm	internal	direct	1.0
¹⁵N	DSS	protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.18 ppm, Outliers: 3 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	4.78 ppm	internal	direct	1.0
¹⁵N	DSS	protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.18 ppm, Outliers: 3 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	4.78 ppm	internal	direct	1.0
¹⁵N	DSS	protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 2 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	4.78 ppm	internal	direct	1.0
¹⁵N	DSS	protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.59 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5IX9, Strand ID: A Detail

Release date

2016-03-30

Citation

Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice
Guo, S., Stevens, C.A., Vance, T., Olijve, L., Graham, L.A., Campbell, R.L., Yazdi, S.R., Escobedo, C., Bar-Dolev, M., Yashunsky, V., Braslavsky, I., Langelaan, D.N., Smith, S.P., Allingham, J.S., Voets, I.K., Davies, P.L.
Sci. Adv. (2017), 3, e1701440-e1701440, PubMed 28808685 , DOI 10.1126/sciadv.1701440 , Abstract

Related entities 1. Antifreeze protein, : 2 entities Detail

Experiments performed 8 experiments Detail

1 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 20 mM TRIS, 50 mM sodium chloride, 2 mM CaCl2, 2 mM MgCl2, 3 mM 13C MpAFP_RINM, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	CaCl2	natural abundance	2 mM
2	MgCl2	natural abundance	2 mM
3	MpAFP_RINM	[U-13C]	3 mM
4	TRIS	natural abundance	20 mM
5	sodium chloride	natural abundance	50 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30040_5ix9.nef
Input source #2: Coordindates	5ix9.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--------9
MSDNQFPFATLGNAIGFITKLDGSVTVQSINGQERVLKLGDPIFFGETVLTGGSGSVTIAFVDGTDVVIGGDSIVEMTDEIYNTGDNEDLVADSSSEIDA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSDNQFPFATLGNAIGFITKLDGSVTVQSINGQERVLKLGDPIFFGETVLTGGSGSVTIAFVDGTDVVIGGDSIVEMTDEIYNTGDNEDLVADSSSEIDA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------100-------110-------120-------130-------140-------150-------160-------170-------180----
LQNAILAGDDPTLIQDAPAAGNTLADQQRVDVSIERNDNSAQAGFGVDTQSSLPTYGYDTDNGNGGQATEREYSAPSLSRTLNQSPLLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LQNAILAGDDPTLIQDAPAAGNTLADQQRVDVSIERNDNSAQAGFGVDTQSSLPTYGYDTDNGNGGQATEREYSAPSLSRTLNQSPLLEHHHHHH
-------110-------120-------130-------140-------150-------160-------170-------180-------190-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	195	0	0	100.0

Content subtype: combined_30040_5ix9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	785		39.0 (chain: A, length: 195)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1984 (1)	noe	38.5 (chain: A, length: 195)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	28 (1)	hbond	16.4 (chain: A, length: 195)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	116 (116)	.	35.9 (chain: A, length: 195)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 195, Sequence coverage: 39.0%
- Total number of assignments
  - ¹H chemical shifts: 386
  - ¹³C chemical shifts: 317
  - ¹⁵N chemical shifts: 82
- Completeness of assignments
- 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: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 195, Sequence coverage: 38.5%
- Total number of restraints: 1972
- Weight of restraints: 1.0 (1972)
- Potential type of restraints: square-well-parabolic (1972)
- Range of distance target values: 1.67, 4.88 (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
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 195, Sequence coverage: 16.4%
  - Total number of restraints: 28
  - Weight of restraints: 1.0 (28)
  - Potential type of restraints: square-well-parabolic (28)
  - Range of distance target values: 2.21, 2.21 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 195, Sequence coverage: 35.9%
- Total number of restraints: 116
- Total number of restraints per polymer type: 116
- Weight of restraints: 1.0 (116)
- Potential type of restraints: square-well-parabolic (116)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords biofilm-associated protein, ice-binding protein

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Found 1 Document (1.417 seconds)

BMRB: 30040

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Antifreeze protein, : 2 entities Detail

Experiments performed 8 experiments Detail

Instrument

Sample

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NMR combined restraints 5 contents Detail