BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 4445

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

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

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

Natural source:   Common Name: Baker   Taxonomy ID: 4932   Superkingdom: not available   Kingdom: not available   Genus/species: Eukaryota Fungi

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

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

Data sets:
Data typeCount
1H chemical shifts1087
13C chemical shifts289
15N chemical shifts158
coupling constants53

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1HRDC1

Entities:

Entity 1, HRDC 91 residues - 10681 Da.

1   METLYSHISHISHISHISHISHISPROMET
2   GLULEUASNASNLEUARGMETTHRTYRGLU
3   ARGLEUARGGLULEUSERLEUASNLEUGLY
4   ASNARGMETVALPROPROVALGLYASNPHE
5   METPROASPSERILELEULYSLYSMETALA
6   ALAILELEUPROMETASNASPSERALAPHE
7   ALATHRLEUGLYTHRVALGLUASPLYSTYR
8   ARGARGARGPHELYSTYRPHELYSALATHR
9   ILEALAASPLEUSERLYSLYSARGSERSER
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:

NameSampleSample stateSample conditions
3D HNCAnot availablenot availableconditions-1
3D CBCA(CO)NHnot availablenot availableconditions-1
3D CBCANHnot availablenot availableconditions-1
3D HCCONH-TOCSYnot availablenot availableconditions-1
3D CCONH-TOCSYnot availablenot availableconditions-1
3D HCCH-TOCSYnot availablenot availableconditions-1
3D proline-edited CDCA(NCO)CAHAnot availablenot availableconditions-1
1H-15N-HSQCnot availablenot availableconditions-1
1H-13C-HMQCnot availablenot availableconditions-1
3D HNHA-Jnot availablenot availableconditions-1
2D HNCGnot availablenot availableconditions-1
2D aromatic (HB)CB(CGCD/CE)HD/HEnot availablenot availableconditions-1
The structures have been directly refined against cross-correlated relaxationnot availablenot availableconditions-1
rates (C-alpha-H-alpha dipole, CO CSA) and the three-bond H/D isotope effect onnot availablenot availableconditions-1
the C-alpha chemical shift. Pulse sequences and experimental details arenot availablenot availableconditions-1
described in reference 3.not availablenot availableconditions-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

Related Database Links:

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