BMRB: 6160

Structural and biochemical evidence for disulfide bond heterogeneity in active forms of the somatomedin B domain of human vitronectin

Authors

Kamikubo, Y., De Guzman, R., Kroon, G., Curriden, Neels, J., Dawson, P., Oldziej, S., Jagielska, A., Scheraga, H., Loskutoff, D., Dyson, H.

Assembly

somatomedin B domain of vitronectin monomer

Entity

1. somatomedin B domain of vitronectin monomer (polymer, Thiol state: all disulfide bound), 51 monomers, 5818.440 Da Detail

DQESCKGRCT EGFNVDKKCQ CDELCSYYQS CCTDYTAECK PQVTRGDVFT M

Formula weight

5818.44 Da

Entity Connection

disulfide 4 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS21:SG
2	disulfide	sing	1:CYS9:SG	1:CYS39:SG
3	disulfide	sing	1:CYS19:SG	1:CYS32:SG
4	disulfide	sing	1:CYS25:SG	1:CYS31:SG

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

torsion angle dynamics in DYANA followed by simulated annealing and energy minimization in AMBER

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.3 %, Completeness (bb): 98.7 % Detail

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Polymer type: polypeptide(L)

	Total	1H	15N
All	94.3 % (329 of 349)	93.5 % (275 of 294)	98.2 % (54 of 55)
Backbone	98.7 % (152 of 154)	99.0 % (103 of 104)	98.0 % (49 of 50)
Sidechain	90.8 % (177 of 195)	90.5 % (172 of 190)	100.0 % (5 of 5)
Aromatic	54.5 % (12 of 22)	54.5 % (12 of 22)
Methyl	100.0 % (14 of 14)	100.0 % (14 of 14)

1. somatomedin B domain of vitronectin

DQESCKGRCT EGFNVDKKCQ CDELCSYYQS CCTDYTAECK PQVTRGDVFT M

Show sample condition

Sample

Temperature 293 (±1) K, pH 7.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	somatomedin B domain of vitronectin	[U-15N]		0.5 mM
2	sodium phosphate			20 mM

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Calculated from 20 models in PDB: 1SSU, Strand ID: A Detail

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Release date

2004-03-24

Citation

Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin
Kamikubo, Y., De Guzman, R., Kroon, G., Curriden, S., Neels, J., Churchill, M., Dawson, P., Oldziej, S., Jagielska, A., Scheraga, H., Loskutoff, D., Dyson, H.
Biochemistry (2004), 43, 6519-6534, PubMed 15157085 , DOI 10.1021/bi049647c , Abstract

Related entities 1. somatomedin B domain of vitronectin monomer, : 1 : 4 : 1 : 16 entities Detail

Interaction partners 1. somatomedin B domain of vitronectin monomer, : 44 interactors Detail

Experiments performed 5 experiments Detail