BMRB Entry 30927

Name: SDE2-apo
Published: 2022-10-03

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PDB ID: 7n99
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30927
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

SDE2-apo

Deposition date:

2021-06-17

Original release date:

2022-10-03

Authors:

Paung, Y.; Weinheimer, A.; Rageul, J.; Khan, A.; Ho, B.; Tong, M.; Johnson, B.; Seeliger, M.; Kim, H.

Citation:

Citation: Weinheimer, Alexandra; Paung, YiTing; Rageul, Julie; Khan, Arafat; Lo, Natalie; Ho, Brian; Tong, Michael; Alphonse, Sebastien; Seeliger, Markus; Kim, Hyungjin. "Extended DNA-binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks" J. Biol. Chem. 298, 102268-102268 (2022).
PubMed: 35850305

Assembly members:

Assembly members:
entity_1, polymer, 77 residues, 8294.899 Da.

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPLGSIDKETIDLLAFTSVA ELELLGLEKLKCELMALGLK CGGTLQERAARLFSVRGLAK EQIDPALFAKPLKGKKK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	301
15N chemical shifts	73
1H chemical shifts	281

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 77 residues - 8294.899 Da.

1

GLY

PRO

LEU

GLY

SER

ILE

ASP

LYS

GLU

THR

2

ILE

ASP

LEU

ALA

PHE

THR

SER

VAL

ALA

3

GLU

LEU

GLU

LEU

GLY

LEU

GLU

LYS

LEU

4

LYS

CYS

GLU

LEU

MET

ALA

LEU

GLY

LEU

LYS

5

CYS

GLY

THR

LEU

GLN

GLU

ARG

ALA

6

ARG

LEU

PHE

SER

VAL

ARG

GLY

LEU

ALA

LYS

7

GLU

GLN

ILE

ASP

PRO

ALA

LEU

PHE

ALA

LYS

8

PRO

LEU

LYS

GLY

LYS

Samples:

sample_1: SDE2-DNA Binding protein, [U-100% 13C; U-100% 15N], 300 uM; Na/K phosphate 50 mM; NaCl 50 mM; DTT 5 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_1	isotropic	sample_conditions_1
3DHNCACO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRFAM-SPARKY, WoongHe, Lee - data analysis

PONDEROSA, Woonghe, Lee - structure calculation

TopSpin, Bruker Biospin - collection

I-PINE, Lee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markley - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III HD 700 MHz
Bruker AVANCE III HD 850 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks