BMRB Entry 16449

Name: Structure of the XPF-single strand DNA complex
Published: 2012-08-03

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PDB ID: 2kn7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16449
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of the XPF-single strand DNA complex

Deposition date:

2009-08-16

Original release date:

2012-08-03

Authors:

Das, Devashish; Folkers, Gert; Dijk, Marc; Jaspers, Nicolaas; Hoeijmakers, Jan; Kaptein, Robert; Boelens, Rolf

Citation:

Citation: Das, Devashish; Folkers, Gert; van Dijk, Marc; Jaspers, Nicolaas; Hoeijmakers, Jan; Kaptein, Robert; Boelens, Rolf. "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." Structure 20, 667-675 (2012).
PubMed: 22483113

Assembly members:

Assembly members:
entity_1, polymer, 134 residues, 14828.994 Da.
DNA, polymer, 10 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pet28B

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: EKYNPGPQDFLLKMPGVNAK NCRSLMHHVKNIAELAALSQ DELTSILGNAANAKQLYDFI HTSFAEVEKYNPGPKDFLLK MPGVNAKNCRSLMHHVKNIA ELAALSQDELTSILGNAANA KQLYDFIHTSFAEV
DNA: CAGTGGCTGA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	199
15N chemical shifts	73
1H chemical shifts	435

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	XPF	1
2	DNA chain	2

Entities:

Entity 1, XPF 134 residues - 14828.994 Da.

1

GLU

LYS

TYR

ASN

PRO

GLY

PRO

GLN

ASP

PHE

2

LEU

LYS

MET

PRO

GLY

VAL

ASN

ALA

LYS

3

ASN

CYS

ARG

SER

LEU

MET

HIS

VAL

LYS

4

ASN

ILE

ALA

GLU

LEU

ALA

LEU

SER

GLN

5

ASP

GLU

LEU

THR

SER

ILE

LEU

GLY

ASN

ALA

6

ALA

ASN

ALA

LYS

GLN

LEU

TYR

ASP

PHE

ILE

7

HIS

THR

SER

PHE

ALA

GLU

VAL

GLU

LYS

TYR

8

ASN

PRO

GLY

PRO

LYS

ASP

PHE

LEU

LYS

9

MET

PRO

GLY

VAL

ASN

ALA

LYS

ASN

CYS

ARG

10

SER

LEU

MET

HIS

VAL

LYS

ASN

ILE

ALA

11

GLU

LEU

ALA

LEU

SER

GLN

ASP

GLU

LEU

12

THR

SER

ILE

LEU

GLY

ASN

ALA

ASN

ALA

13

LYS

GLN

LEU

TYR

ASP

PHE

ILE

HIS

THR

SER

14

PHE

ALA

GLU

VAL

Entity 2, DNA chain 10 residues - Formula weight is not available

1

DC

DA

DG

DT

DG

DC

DT

DG

DA

Samples:

XPF-ssDNAcomplex: sodium phosphate 80 mM; sodium chloride 2 mM; AEBSF protease inhibitor5 – 10 uM

sample_conditions_1: ionic strength: 100 mM; pH: 5.2; pressure: 1 atm; temperature: 293.6 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY	XPF-ssDNAcomplex	isotropic	sample_conditions_1
3D 1H-15N NOESY	XPF-ssDNAcomplex	isotropic	sample_conditions_1
3D CBCA(CO)NH	XPF-ssDNAcomplex	isotropic	sample_conditions_1
2D 1H-15N HSQC	XPF-ssDNAcomplex	isotropic	sample_conditions_1
2D 1H-13C HSQC	XPF-ssDNAcomplex	isotropic	sample_conditions_1
3D HCCH-TOCSY	XPF-ssDNAcomplex	isotropic	sample_conditions_1
3D C(CO)NH	XPF-ssDNAcomplex	isotropic	sample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - processing

CYANA, Herrmann, Guntert and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker Avance 900 MHz
Bruker DRX 600 MHz