BMRB Entry 51696

Name: Backbone chemical shift assignment of yeast expressed NIST-Fab light and heavy chain
Published: 2023-03-01

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51696

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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:

Backbone chemical shift assignment of yeast expressed NIST-Fab light and heavy chain

Deposition date:

2022-11-15

Original release date:

2023-03-01

Authors:

Solomon, Tsega; Brinson, Robert

Citation:

Citation: Solomon, Tsega; Chao, Kinlin; Gingras, Genevieve; Aubin, Yves; O'Dell, W. Brad; Marino, John; Brinson, Robert. "Backbone NMR assignment of the yeast expressed Fab fragment of the NISTmAb reference antibody" Biomol. NMR Assign. 17, 75-81 (2023).
PubMed: 36856943

Assembly members:

Assembly members:
entity_1, polymer, 217 residues, Formula weight is not available
entity_2, polymer, 231 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Pichia pastoris Vector: pPICZ-A

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: EAEADIQMTQSPSTLSASVG DRVTITCSASSRVGYMHWYQ QKPGKAPKLLIYDTSKLASG VPSRFSGSGSGTEFTLTISS LQPDDFATYYCFQGSGYPFT FGGGTKVEIKRTVAAPSVFI FPPSDEQLKSGTASVVCLLN NFYPREAKVQWKVDNALQSG NSQESVTEQDSKDSTYSLSS TLTLSKADYEKHKVYACEVT HQGLSSPVTKSFNRGEC
entity_2: EAEAQVTLRESGPALVKPTQ TLTLTCTFSGFSLSTAGMSV GWIRQPPGKALEWLADIWWD DKKHYNPSLKDRLTISKDTS KNQVVLKVTNMDPADTATYY CARDMIFNFYFDVWGQGTTV TVSSASTKGPSVFPLAPSSK STSGGTAALGCLVKDYFPEP VTVSWNSGALTSGVHTFPAV LQSSGLYSLSSVVTVPSSSL GTQTYICNVNHKPSNTKVDK RVEPKSCDKTH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	1231
15N chemical shifts	398
1H chemical shifts	398

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	NIST-Fab, Chain 1	1
2	NIST-Fab, Chain 2	2

Entities:

Entity 1, NIST-Fab, Chain 1 217 residues - Formula weight is not available

Residue 1 begins at D

1

GLU

ALA

GLU

ALA

ASP

ILE

GLN

MET

THR

GLN

2

SER

PRO

SER

THR

LEU

SER

ALA

SER

VAL

GLY

3

ASP

ARG

VAL

THR

ILE

THR

CYS

SER

ALA

SER

4

SER

ARG

VAL

GLY

TYR

MET

HIS

TRP

TYR

GLN

5

GLN

LYS

PRO

GLY

LYS

ALA

PRO

LYS

LEU

6

ILE

TYR

ASP

THR

SER

LYS

LEU

ALA

SER

GLY

7

VAL

PRO

SER

ARG

PHE

SER

GLY

SER

GLY

SER

8

GLY

THR

GLU

PHE

THR

LEU

THR

ILE

SER

9

LEU

GLN

PRO

ASP

PHE

ALA

THR

TYR

10

CYS

PHE

GLN

GLY

SER

GLY

TYR

PRO

PHE

THR

11

PHE

GLY

THR

LYS

VAL

GLU

ILE

LYS

12

ARG

THR

VAL

ALA

PRO

SER

VAL

PHE

ILE

13

PHE

PRO

SER

ASP

GLU

GLN

LEU

LYS

SER

14

GLY

THR

ALA

SER

VAL

CYS

LEU

ASN

15

ASN

PHE

TYR

PRO

ARG

GLU

ALA

LYS

VAL

GLN

16

TRP

LYS

VAL

ASP

ASN

ALA

LEU

GLN

SER

GLY

17

ASN

SER

GLN

GLU

SER

VAL

THR

GLU

GLN

ASP

18

SER

LYS

ASP

SER

THR

TYR

SER

LEU

SER

19

THR

LEU

THR

LEU

SER

LYS

ALA

ASP

TYR

GLU

20

LYS

HIS

LYS

VAL

TYR

ALA

CYS

GLU

VAL

THR

21

HIS

GLN

GLY

LEU

SER

PRO

VAL

THR

LYS

22

SER

PHE

ASN

ARG

GLY

GLU

CYS

Entity 2, NIST-Fab, Chain 2 231 residues - Formula weight is not available

Residue 1 begins at Q

1

GLU

ALA

GLU

ALA

GLN

VAL

THR

LEU

ARG

GLU

2

SER

GLY

PRO

ALA

LEU

VAL

LYS

PRO

THR

GLN

3

THR

LEU

THR

LEU

THR

CYS

THR

PHE

SER

GLY

4

PHE

SER

LEU

SER

THR

ALA

GLY

MET

SER

VAL

5

GLY

TRP

ILE

ARG

GLN

PRO

GLY

LYS

ALA

6

LEU

GLU

TRP

LEU

ALA

ASP

ILE

TRP

ASP

7

ASP

LYS

HIS

TYR

ASN

PRO

SER

LEU

LYS

8

ASP

ARG

LEU

THR

ILE

SER

LYS

ASP

THR

SER

9

LYS

ASN

GLN

VAL

LEU

LYS

VAL

THR

ASN

10

MET

ASP

PRO

ALA

ASP

THR

ALA

THR

TYR

11

CYS

ALA

ARG

ASP

MET

ILE

PHE

ASN

PHE

TYR

12

PHE

ASP

VAL

TRP

GLY

GLN

GLY

THR

VAL

13

THR

VAL

SER

ALA

SER

THR

LYS

GLY

PRO

14

SER

VAL

PHE

PRO

LEU

ALA

PRO

SER

LYS

15

SER

THR

SER

GLY

THR

ALA

LEU

GLY

16

CYS

LEU

VAL

LYS

ASP

TYR

PHE

PRO

GLU

PRO

17

VAL

THR

VAL

SER

TRP

ASN

SER

GLY

ALA

LEU

18

THR

SER

GLY

VAL

HIS

THR

PHE

PRO

ALA

VAL

19

LEU

GLN

SER

GLY

LEU

TYR

SER

LEU

SER

20

SER

VAL

THR

VAL

PRO

SER

LEU

21

GLY

THR

GLN

THR

TYR

ILE

CYS

ASN

VAL

ASN

22

HIS

LYS

PRO

SER

ASN

THR

LYS

VAL

ASP

LYS

23

ARG

VAL

GLU

PRO

LYS

SER

CYS

ASP

LYS

THR

24

HIS

Samples:

sample_1: Chain 1, [U-100% 13C; U-100% 15N; U-80% 2H], 2.65 mM; Chain 2, [U-100% 13C; U-100% 15N; U-80% 2H], 2.65 mM; Bis-Tris 25 mM; DSS, [U-2H], 150 uM; D2O, [U-100% 2H], 3%

sample_conditions_1: ionic strength: 0.025 M; pH: 6; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D (H)N(CA)NNH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v3.6.1 - collection

NMRFAM-SPARKY - chemical shift assignment

NMRPipe - processing

NMR spectrometers:

Bruker AVANCE III 900 MHz
Bruker AVANCE III 600 MHz

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