BMRB Entry 4445

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PDB ID: 1d8b
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR4445
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

1H, 13C, and 15N Chemical Shift Assignments and coupling constants for the HRDC domain from S. cerevisiae Sgs1 RecQ helicase

Deposition date:

1999-10-22

Original release date:

2000-07-18

Authors:

Liu, Zhihong; Macias, Maria; Bottomley, Matthew; Stier, Gunter; Linge, Jens; Nilges, Michael; Bork, Peer; Sattler, Michael

Citation:

Citation: Liu, Zhihong; Macias, Maria; Bottomley, Matthew; Stier, Gunter; Linge, Jens; Nilges, Michael; Bork, Peer; Sattler, Michael. "The 3D structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins." Structure 7, 1557-1566 (1999).

Assembly members:

Assembly members:
HRDC domain of Sgs1 RecQ helicase, polymer, 91 residues, 10681 Da.

Natural source:

Natural source: Common Name: Baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET9D

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HRDC domain of Sgs1 RecQ helicase: MKHHHHHHPMELNNLRMTYE RLRELSLNLGNRMVPPVGNF MPDSILKKMAAILPMNDSAF ATLGTVEDKYRRRFKYFKAT IADLSKKRSSE

Data sets:

assigned_chemical_shifts
- shift_set_1
- shift_set_2
coupling_constants
- coupling_constants

Data type	Count
1H chemical shifts	1087
13C chemical shifts	289
15N chemical shifts	158
coupling constants	53

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HRDC	1

Entities:

Entity 1, HRDC 91 residues - 10681 Da.

1

MET

LYS

HIS

PRO

MET

2

GLU

LEU

ASN

LEU

ARG

MET

THR

TYR

GLU

3

ARG

LEU

ARG

GLU

LEU

SER

LEU

ASN

LEU

GLY

4

ASN

ARG

MET

VAL

PRO

VAL

GLY

ASN

PHE

5

MET

PRO

ASP

SER

ILE

LEU

LYS

MET

ALA

6

ALA

ILE

LEU

PRO

MET

ASN

ASP

SER

ALA

PHE

7

ALA

THR

LEU

GLY

THR

VAL

GLU

ASP

LYS

TYR

8

ARG

PHE

LYS

TYR

PHE

LYS

ALA

THR

9

ILE

ALA

ASP

LEU

SER

LYS

ARG

SER

10

GLU

Samples:

sample_1: HRDC domain of Sgs1 RecQ helicase, [U-15N], 1.5 – 1.8 mM; sodium phosphate 20 mM; H2O 90%; D2O 10%

sample_2: HRDC domain of Sgs1 RecQ helicase, [U-13C; U-15N], 1.5 – 1.8 mM; sodium phosphate 20 mM; D2O 100%

sample_3: HRDC domain of Sgs1 RecQ helicase, [U-13C; U-15N], 1.3 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.02%; D2O 50%; H2O 50%

conditions-1: pH: 6.5; temperature: 295 K; ionic strength: 20 mM; pressure: 1 atm; solvent exchange time: 2592000 s

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	not available	not available	conditions-1
3D CBCA(CO)NH	not available	not available	conditions-1
3D CBCANH	not available	not available	conditions-1
3D HCCONH-TOCSY	not available	not available	conditions-1
3D CCONH-TOCSY	not available	not available	conditions-1
3D HCCH-TOCSY	not available	not available	conditions-1
3D proline-edited CDCA(NCO)CAHA	not available	not available	conditions-1
1H-15N-HSQC	not available	not available	conditions-1
1H-13C-HMQC	not available	not available	conditions-1
3D HNHA-J	not available	not available	conditions-1
2D HNCG	not available	not available	conditions-1
2D aromatic (HB)CB(CGCD/CE)HD/HE	not available	not available	conditions-1
The structures have been directly refined against cross-correlated relaxation	not available	not available	conditions-1
rates (C-alpha-H-alpha dipole, CO CSA) and the three-bond H/D isotope effect on	not available	not available	conditions-1
the C-alpha chemical shift. Pulse sequences and experimental details are	not available	not available	conditions-1
described in reference 3.	not available	not available	conditions-1

Software:

NMRPIPE v1.7 - spectra processing

XEASY v1.3.13 - spectra assignment

ARIA v0.9 - automated NOE assignment, structure calculation, structure analysis, Starting with an almost complete list of chemical shifts, some few assigned NOEs and otherwise uninterpreted NOE peak lists, the program ARIA (Ambiguous Restraints in Iterative Assignment) calibrates NOEs, merges the obtained ambiguous distance restraints from different NOE spectra and assigns the NOE peaks in an iterative manner.

CNS v0.9 - structure calculation

CAPP v4.0.7 - Isotope Effect

PIPP v4.0.7 - Isotope Effect

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DRX 600 MHz

PDB	1D8B
DBJ	GAA25638
EMBL	CAA87811 CAY82020
GB	AAA35167 AAB60289 AHY76643 AJP40883 AJS62054
REF	NP_013915
SP	P35187
TPG	DAA10088
AlphaFold	P35187