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BMRB: 16449

2KN7

Structure of the XPF-single strand DNA complex

Authors

Das, D., Folkers, G.E., Dijk, M.V., Jaspers, N.G.J., Hoeijmakers, J.H.J., Kaptein, R., Boelens, R.

Assembly

XPF DNA complex

Entity

1. XPF DNA complex, entity 1 (polymer, Thiol state: all free), 134 monomers, 14810.76 Da Detail

EKYNPGPQDF LLKMPGVNAK NCRSLMHHVK NIAELAALSQ DELTSILGNA ANAKQLYDFI HTSFAEVEKY NPGPKDFLLK MPGVNAKNCR SLMHHVKNIA ELAALSQDEL TSILGNAANA KQLYDFIHTS FAEV

2. DNA (polymer, Thiol state: not present), 10 monomers, 3148.000 Da Detail

CAGTGGCTGA

Total weight

17958.76 Da

Max. entity weight

14810.76 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 52.8 %, Completeness: 42.7 %, Completeness (bb): 42.8 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	42.7 % (707 of 1657)	43.4 % (393 of 906)	38.9 % (236 of 606)	53.8 % (78 of 145)
Backbone	42.8 % (369 of 862)	42.3 % (143 of 338)	39.6 % (157 of 396)	53.9 % (69 of 128)
Sidechain	44.3 % (409 of 923)	44.0 % (250 of 568)	44.4 % (150 of 338)	52.9 % (9 of 17)
Aromatic	26.5 % (36 of 136)	32.1 % (25 of 78)	19.0 % (11 of 58)
Methyl	50.6 % (78 of 154)	48.7 % (38 of 78)	52.6 % (40 of 76)

1. entity 1

EKYNPGPQDF LLKMPGVNAK NCRSLMHHVK NIAELAALSQ DELTSILGNA ANAKQLYDFI HTSFAEVEKY NPGPKDFLLK MPGVNAKNCR SLMHHVKNIA ELAALSQDEL TSILGNAANA KQLYDFIHTS FAEV

2. DNA

CAGTGGCTGA

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293.6 K, pH 5.2 (±0.2)

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	80 mM
2	sodium chloride	natural abundance	2 mM
3	AEBSF protease inhibitor	natural abundance	5.0 ~ 10.0 uM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	na	direct	0.0
¹H	water	protons	external	direct	1.0
¹⁵N	water	protons	na	direct	0.0

Referencing offset: -1.64 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	na	direct	0.0
¹H	water	protons	external	direct	1.0
¹⁵N	water	protons	na	direct	0.0

Referencing offset: -1.64 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	na	direct	0.0
¹H	water	protons	external	direct	1.0
¹⁵N	water	protons	na	direct	0.0

Referencing offset: -0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KN7, Strand ID: A, D Detail

Release date

2012-08-02

Citation

The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition
Das, D., Folkers, G.E., van Dijk, M., Jaspers, N.G.J., Hoeijmakers, J.H.J., Kaptein, R., Boelens, R.
Structure (2012), 20, 667-675, PubMed 22483113 , DOI 10.1016/j.str.2012.02.009 , Abstract

Related entities 1. XPF DNA complex, entity 1, : 2 entities Detail

Experiments performed 7 experiments Detail

1 3D 1H-13C NOESY