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 15913

Title: Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin   PubMed: 18715872

Authors: Villareal, Valerie; Pilpa, Rosemarie; Robson, Scott; Fadeev, Evgeny; Clubb, Robert

Citation: Villareal, Valerie; Pilpa, Rosemarie; Robson, Scott; Fadeev, Evgeny; Clubb, Robert. "The IsdC protein from Staphylococcus aureus uses a flexible binding pocket to capture heme"  J. Biol. Chem. 283, 31591-31600 (2008).

Assembly members:
IsdC, polymer, 147 residues, 14322.988 Da.
ZNH, non-polymer, 626.051 Da.

Natural source:   Common Name: Staphylococcus aureus   Taxonomy ID: 1280   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Staphylococcus aureus

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

Entity Sequences (FASTA):
IsdC: MGSSHHHHHHSSGLVPRGSH MSANAADSGTLNYEVYKYNT NDTSIANDYFNKPAKYIKKN GKLYVQITVNHSHWITGMSI EGHKENIISKNTAKDERTSE FEVSKLNGKIDGKIDVYIDE KVNGKPFKYDHHYNITYKFN GPTDVAG

Data sets:
Data typeCount
13C chemical shifts488
15N chemical shifts130
1H chemical shifts730

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1IsdC1
2ZNH2

Entities:

Entity 1, IsdC 147 residues - 14322.988 Da.

Residues 4-24 represent a Histidine-tag that was not included in the structure calculations

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METSERALAASNALAALAASPSERGLYTHR
4   LEUASNTYRGLUVALTYRLYSTYRASNTHR
5   ASNASPTHRSERILEALAASNASPTYRPHE
6   ASNLYSPROALALYSTYRILELYSLYSASN
7   GLYLYSLEUTYRVALGLNILETHRVALASN
8   HISSERHISTRPILETHRGLYMETSERILE
9   GLUGLYHISLYSGLUASNILEILESERLYS
10   ASNTHRALALYSASPGLUARGTHRSERGLU
11   PHEGLUVALSERLYSLEUASNGLYLYSILE
12   ASPGLYLYSILEASPVALTYRILEASPGLU
13   LYSVALASNGLYLYSPROPHELYSTYRASP
14   HISHISTYRASNILETHRTYRLYSPHEASN
15   GLYPROTHRASPVALALAGLY

Entity 2, ZNH - C34 H32 N4 O4 Zn - 626.051 Da.

1   ZNH

Samples:

sample_1: sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 0.01%; IsdC, [U-100% 13C; U-100% 15N], 1.3 mM; ZNH 2.1 mM; D2O, [U-100% 2H], 7%; H2O 93%

sample_2: sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 0.01%; IsdC 1.1 mM; ZNH 2.3 mM; D2O 100%

sample_conditions_1: ionic strength: 150 mM; pH: 6; pressure: 1 atm; temperature: 302 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

PIPP, Garrett - peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

ATHNOS-CANDID, Herrmann, Guntert, Wuthrich - chemical shift assignment

CARA, Keller - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
DBJ BAB42227 BAB57293 BAB94878 BAF67314 BAF78005
EMBL CAG40106 CAG42839 CAI80683 CAQ49552 CBI49004
GB AAL33767 AAW38020 ABD20415 ABD30198 ABQ48990
REF WP_000789795 WP_000789808 WP_000789809 WP_000789810 WP_000789811
SP A5IS17 A6QG32 A6U0U8 A7X149 A8Z1R1