BMRBj - BMREntryMaster

Found 1 Document (1.413 seconds)

BMRB: 5573

1N4I

Spruce budworm Antifreeze Protein: Changes in Structure and Dynamics at Low Temperature

Authors

Graether, S.P., Gagne, S.M., Spyracopoulos, L., Jia, Z., Sykes, B.D., Davies, P.L.

Assembly

spruce budworm antifreeze protein

Entity

1. spruce budworm antifreeze protein (polymer, Thiol state: free and disulfide bound), 90 monomers, 9060.971 Da Detail

DGSCTNTNSQ LSANSKCEKS TLTNCYVDKS EVYGTTCTGS RFDGVTITTS TSTGSRISGP GCKISTCIIT GGVPAPSAAC KISGCTFSAN

Formula weight

9060.971 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	0:CYS4:SG	1:CYS17:SG
2	disulfide	sing	0:CYS25:SG	1:CYS37:SG
3	disulfide	sing	0:CYS62:SG	1:CYS85:SG
4	disulfide	sing	0:CYS67:SG	1:CYS80:SG

Source organism

Choristoneura fumiferana

Exptl. method

NMR

Refine. method

Simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.7 %, Completeness (bb): 93.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.7 % (784 of 904)	84.3 % (386 of 458)	89.5 % (316 of 353)	88.2 % (82 of 93)
Backbone	93.1 % (497 of 534)	89.8 % (168 of 187)	95.4 % (248 of 260)	93.1 % (81 of 87)
Sidechain	80.7 % (363 of 450)	80.4 % (218 of 271)	83.2 % (144 of 173)	16.7 % (1 of 6)
Aromatic	27.8 % (10 of 36)	55.6 % (10 of 18)	0.0 % (0 of 18)
Methyl	95.5 % (84 of 88)	93.2 % (41 of 44)	97.7 % (43 of 44)

1. spruce budworm antifreeze protein

DGSCTNTNSQ LSANSKCEKS TLTNCYVDKS EVYGTTCTGS RFDGVTITTS TSTGSRISGP GCKISTCIIT GGVPAPSAAC KISGCTFSAN

Show sample condition

Sample

Temperature 298 (±0.1) K, pH 5.5 (±0.25)

#	Name	Isotope labeling	Type	Concentration
1	spruce budworm antifreeze protein	[U-15N; U-13C]		18 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: -0.33 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 1.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 25 models in PDB: 1N4I, Strand ID: A Detail

Release date

2003-05-13

Citation 1

Spruce budworm antifreeze protein: changes in structure and dynamics at low temperature
Graether, S.P., Gagne, S.M., Spyracopoulos, L., Jia, Z., Davies, P.L., Sykes, B.D.
J. Mol. Biol. (2003), 327, 1155-1168, PubMed 12662938 , DOI: , Abstract

Show more 1 citaion

Citation 2

Beta-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect
Nature (2000), 406, 325-328, PubMed 10917537 , DOI 10.1038/35018610 , Abstract

Hide non-primary 1 citaion

Entries sharing articles BMRB: 1 entries Detail

BMRB: 5572 released on 2002-12-26
Title Beta-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect

Related entities 1. spruce budworm antifreeze protein, : 1 : 1 : 4 entities Detail

Experiments performed 1 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr5573_3.str
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)
1:4:CYS:SG	1:17:CYS:SG	oxidized, CA 52.15, CB 39.73 ppm	unknown	n/a
1:25:CYS:SG	1:37:CYS:SG	oxidized, CA 55.43, CB 49.49 ppm	oxidized, CA 56.37, CB 42.98 ppm	n/a
1:62:CYS:SG	1:85:CYS:SG	oxidized, CA 55.28, CB 37.5 ppm	oxidized, CA 55.41, CB 47.89 ppm	n/a
1:67:CYS:SG	1:80:CYS:SG	oxidized, CA 55.03, CB 49.67 ppm	oxidized, CA 55.72, CB 37.88 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr5573_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	865		100.0 (chain: 1, length: 90)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 90, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 467
  - ¹³C chemical shifts: 316
  - ¹⁵N chemical shifts: 82
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	458	385	84.1
¹³C chemical shifts	353	316	89.5
¹⁵N chemical shifts	95	82	86.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	187	169	90.4
¹³C chemical shifts	180	172	95.6
¹⁵N chemical shifts	87	81	93.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	271	216	79.7
¹³C chemical shifts	173	144	83.2
¹⁵N chemical shifts	8	1	12.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	41	93.2
¹³C chemical shifts	44	43	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	10	55.6
¹³C chemical shifts	18	0	0.0

Keywords antifreeze, ice, beta-helix

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Found 1 Document (1.413 seconds)

BMRB: 5573

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. spruce budworm antifreeze protein, : 1 : 1 : 4 entities Detail

Experiments performed 1 experiments Detail

Instrument

Sample

Chemical shift validation 3 contents Detail