BMRB Entry 31183

Name: Solution NMR structure of apo I89, a dynamic engineered calcium-binding protein (state 2)
Published: 2025-05-29

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PDB ID: 9cid
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31183
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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:

Solution NMR structure of apo I89, a dynamic engineered calcium-binding protein (state 2)

Deposition date:

2024-07-03

Original release date:

2025-05-29

Authors:

Guo, A.; Kelly, M.; Kortemme, T.

Citation:

Citation: Guo, Amy; Akpinaroglu, Deniz; Stephens, Christina; Grabe, Michael; Smith, Colin; Kelly, Mark; Kortemme, Tanja. "Deep learning-guided design of dynamic proteins" Science 388, eadr7094-eadr7094 (2025).
PubMed: 40403060

Assembly members:

Assembly members:
entity_1, polymer, 94 residues, 10421.816 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pET-28a(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSHMASMEDLQAEARAFLSE EMIAEFKAAFDMFDADGGGD ISYKAVGTVFRMLGINPSKE VLDYLKEKIDVDGSGTIDFE EFLVLMVYIMKQDA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	300
15N chemical shifts	92
1H chemical shifts	642

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 94 residues - 10421.816 Da.

1

GLY

SER

HIS

MET

ALA

SER

MET

GLU

ASP

LEU

2

GLN

ALA

GLU

ALA

ARG

ALA

PHE

LEU

SER

GLU

3

GLU

MET

ILE

ALA

GLU

PHE

LYS

ALA

PHE

4

ASP

MET

PHE

ASP

ALA

ASP

GLY

ASP

5

ILE

SER

TYR

LYS

ALA

VAL

GLY

THR

VAL

PHE

6

ARG

MET

LEU

GLY

ILE

ASN

PRO

SER

LYS

GLU

7

VAL

LEU

ASP

TYR

LEU

LYS

GLU

LYS

ILE

ASP

8

VAL

ASP

GLY

SER

GLY

THR

ILE

ASP

PHE

GLU

9

GLU

PHE

LEU

VAL

LEU

MET

VAL

TYR

ILE

MET

10

LYS

GLN

ASP

ALA

Samples:

sample_1: I89, [U-99% 13C; U-99% 15N], 400 uM; potassium chloride 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.7; pressure: 1 atm; temperature: 298.1 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HBCBCGCDCEHE	sample_1	isotropic	sample_conditions_1
3D HBCBCGCDHD	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1

Software:

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

ARTINA, Klukowski, P., Riek, R. and Guntert, P. - chemical shift assignment, peak picking, structure calculation

NMR spectrometers:

Bruker AVANCE 600 MHz
Bruker AVANCE 800 MHz

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