BMRB Entry 18423

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

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR18423

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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 (ferric form with heme PTM, cyanide 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_CYN, non-polymer, 26.017 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
15N chemical shifts	135
1H chemical shifts	400
heteronuclear NOE values	93
T1 relaxation values	103
T2 relaxation values	101

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

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 N - 26.017 Da.

1

CYN

Samples:

sample_1: GlbN, [U-15N], 1.3 mM; HEB 1.3 mM; potassium phosphate 20 mM; potassium cyanide 65 mM

sample_2: GlbN 1 mM; HEB 1 mM; potassium phosphate 20 mM; potassium cyanide 10 mM

sample_3: GlbN 1.3 mM; HEB 1.3 mM; potassium cyanide 13 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 7.2; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 0.1 M; pH*: 7.3; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.15 M; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_3	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_3
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_3
2D 1H-15N NOE	sample_1	isotropic	sample_conditions_1
2D 15N R1	sample_1	isotropic	sample_conditions_1
2D 15N R2	sample_1	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
Bruker DRX 600 MHz

REF	YP_001734867 WP_012307234 WP_030006991
BMRB	16306 16307 17947 18422 18424
PDB	2KSC 4L2M 4MAX
GB	AAL79195 ACA99611