BMRB Entry 18422

Name: Backbone dynamics of the truncated (2/2) hemoglobin from Synechococcus sp. PCC 7002 (ferrous form with heme PTM, carbonmonoxy complex)
Published: 2012-05-02

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18422

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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 dynamics of the truncated (2/2) hemoglobin from Synechococcus sp. PCC 7002 (ferrous form with heme PTM, carbonmonoxy complex)

Deposition date:

2012-04-24

Original release date:

2012-05-02

Authors:

Lecomte, Juliette; Pond, Matthew; Majumdar, Ananya

Citation:

Citation: Wenke, Belinda; Lecomte, Juliette; Heroux, Annie; Schlessman, Jamie. "The 2/2 hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002 with covalently attached heme: comparison of X-ray and NMR structures." Proteins 82, 528-534 (2014).
PubMed: 23999883

Assembly members:

Assembly members:
entity_HEB, non-polymer, 618.503 Da.
GlbN, polymer, 123 residues, Formula weight is not available
entity_CMO, non-polymer, 28.010 Da.

Natural source:

Natural source: Common Name: Synechococcus sp. PCC 7002 Taxonomy ID: 32049 Superkingdom: Bacteria Kingdom: not available Genus/species: cyanobacteria synechococcus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET3c

Entity Sequences (FASTA):

Entity Sequences (FASTA):
GlbN: ASLYEKLGGAAAVDLAVEKF YGKVLADERVNRFFVNTDMA KQKQHQKDFMTYAFGGTDRF PGRSMRAAHQDLVENAGLTD VHFDAIAENLVLTLQELNVS QDLIDEVVTIVGSVQHRNDV LNR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shifts_list_2
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1

Data type	Count
13C chemical shifts	348
15N chemical shifts	134
1H chemical shifts	497
heteronuclear NOE values	90
T1 relaxation values	92
T2 relaxation values	94

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	GlbN	2
2	prosthetic group	1
3	ligand	3

Entities:

Entity 2, GlbN 123 residues - Formula weight is not available

1

ALA

SER

LEU

TYR

GLU

LYS

LEU

GLY

ALA

2

ALA

VAL

ASP

LEU

ALA

VAL

GLU

LYS

PHE

3

TYR

GLY

LYS

VAL

LEU

ALA

ASP

GLU

ARG

VAL

4

ASN

ARG

PHE

VAL

ASN

THR

ASP

MET

ALA

5

LYS

GLN

LYS

GLN

HIS

GLN

LYS

ASP

PHE

MET

6

THR

TYR

ALA

PHE

GLY

THR

ASP

ARG

PHE

7

PRO

GLY

ARG

SER

MET

ARG

ALA

HIS

GLN

8

ASP

LEU

VAL

GLU

ASN

ALA

GLY

LEU

THR

ASP

9

VAL

HIS

PHE

ASP

ALA

ILE

ALA

GLU

ASN

LEU

10

VAL

LEU

THR

LEU

GLN

GLU

LEU

ASN

VAL

SER

11

GLN

ASP

LEU

ILE

ASP

GLU

VAL

THR

ILE

12

VAL

GLY

SER

VAL

GLN

HIS

ARG

ASN

ASP

VAL

13

LEU

ASN

ARG

Entity 1, prosthetic group - C34 H34 Fe N4 O4 - 618.503 Da.

1

HEB

Entity 3, ligand - C O - 28.010 Da.

1

CMO

Samples:

sample_1: GlbN, [U-13C; U-15N], 0.7 mM; HEB 0.7 mM; potassium phosphate 20 mM; dithionite 7 mM; CO 0.7-1.6 mM

sample_2: GlbN, [U-15N], 1.8 mM; HEB 1.8 mM; potassium phosphate 20 mM; dithionite 18 mM; CO 1.8-2.7 mM

sample_3: GlbN, [U-15N], 1 mM; HEB 1 mM; potassium phosphate 20 mM; dithionite 10 mM; CO 1-1.8 mM

sample_4: GlbN 0.9 mM; HEB 0.9 mM; potassium phosphate 100 mM; dithionite 14 mM; CO 0.9-1.8 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 7.3; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 0.3 M; pH*: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_4	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_3
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_3
2D DQF-COSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-15N NOE	sample_3	isotropic	sample_conditions_1
2D 15N R1	sample_2	isotropic	sample_conditions_1
2D 15N R2	sample_3	isotropic	sample_conditions_1

Software:

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

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz

REF	YP_001734867 WP_012307234 WP_030006991
BMRB	16306 16307 17947 18423 18424
PDB	2KSC 4L2M 4MAX
GB	AAL79195 ACA99611