BMRB Entry 17862

Name: Solution structure of Staphylococcus aureus IsdH linker domain
Published: 2012-06-19

Click here to enlarge.

PDB ID: 2lhr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: LACS
BMRB Entry DOI: doi:10.13018/BMR17862
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Solution structure of Staphylococcus aureus IsdH linker domain

Deposition date:

2011-08-12

Original release date:

2012-06-19

Authors:

Spirig, Thomas; Clubb, Robert; Malmirchegini, G.; Robson, Scott

Citation:

Citation: Krishna Kumar, Kaavya; Jacques, David; Pishchany, Gleb; Caradoc-Davies, Tom; Spirig, Thomas; Malmirchegini, G. Reza; Langley, David; Dickson, Claire; Mackay, Joel; Clubb, Robert; Skaar, Eric; Guss, J. Mitchell; Gell, David. "Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH." J. Biol. Chem. 286, 38439-38447 (2011).
PubMed: 21917915

Assembly members:

Assembly members:
entity, polymer, 78 residues, 9280.425 Da.

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: SDDYVDEETYNLQKLLAPYH KAKTLERQVYELEKLQEKLP EKYKAEYKKKLDQTRVELAD QVKSAVTEFENVTPTNDQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	357
15N chemical shifts	82
1H chemical shifts	568

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Staphylococcus aureus IsdH linker domain	1

Entities:

Entity 1, Staphylococcus aureus IsdH linker domain 78 residues - 9280.425 Da.

Residue 1 represents a non-native residue left after cleaving of the affinity tag

1

SER

ASP

TYR

VAL

ASP

GLU

THR

TYR

2

ASN

LEU

GLN

LYS

LEU

ALA

PRO

TYR

HIS

3

LYS

ALA

LYS

THR

LEU

GLU

ARG

GLN

VAL

TYR

4

GLU

LEU

GLU

LYS

LEU

GLN

GLU

LYS

LEU

PRO

5

GLU

LYS

TYR

LYS

ALA

GLU

TYR

LYS

6

LEU

ASP

GLN

THR

ARG

VAL

GLU

LEU

ALA

ASP

7

GLN

VAL

LYS

SER

ALA

VAL

THR

GLU

PHE

GLU

8

ASN

VAL

THR

PRO

THR

ASN

ASP

GLN

Samples:

sample_1: IsdH linker, [U-100% 15N], 1.1 mM; potassium phosphate 20 mM; potassium chloride 50 mM; AEBSF protease inhibitor 100 uM; sodium azide 0.01%; D2O 7%; H2O 93%

sample_2: IsdH linker, [U-100% 13C; U-100% 15N], 1.3 mM; potassium phosphate 20 mM; potassium chloride 50 mM; AEBSF protease inhibitor 100 uM; sodium azide 0.01%; D2O 7%; H2O 93%

sample_3: IsdH linker, [U-100% 13C; U-100% 15N], 1.3 mM; potassium phosphate 20 mM; potassium chloride 50 mM; AEBSF protease inhibitor 100 uM; sodium azide 0.01%; D2O 100%

sample_conditions_1: ionic strength: 140 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D CC(CO)NH	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
2D CB(CGCD)HD	sample_3	isotropic	sample_conditions_1
2D CB(CGCD)HE	sample_3	isotropic	sample_conditions_1

Software:

PIPP, Garrett - peak picking

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

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

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

UNIO, Herrmann, Guntert and Wuthrich - chemical shift assignment

ProcheckNMR, Laskowski and MacArthur - geometry optimization

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

xwinnmr, Bruker Biospin - collection

CARA, Keller - chemical shift assignment

NMR spectrometers:

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

BMRB	17820
PDB	2LHR 4IJ2 4XS0
DBJ	BAB42820 BAB57893 BAB95538 BAF67896 BAF78600
EMBL	CAG43459 CAI81279 CAQ50207 CBI49597 CBX34951
GB	AAW38309 ABD20516 ABD30910 ABQ49576 ABR52665
REF	WP_001032759 WP_001032760 WP_001032761 WP_001032762 WP_001032763
SP	Q2FG07 Q2FXJ2 Q2YTF7 Q5HF43 Q6G8J7
AlphaFold	Q2FG07 Q2FXJ2 Q2YTF7 Q5HF43 Q6G8J7