4L2M

Crystal structure of the 2/2 hemoglobin from Synechococcus sp. PCC 7002 in the cyanomet state and with covalently attached heme

PDB DOI: https://doi.org/10.2210/pdb4L2M/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Picosynechococcus sp. PCC 7002
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-06-04 Released: 2013-06-12
Deposition Author(s): Wenke, B.B., Schlessman, J.L., Heroux, A., Lecomte, J.T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.288
R-Value Work: 0.218
R-Value Observed: 0.221

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The 2/2 hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002 with covalently attached heme: Comparison of X-ray and NMR structures.

Wenke, B.B., Lecomte, J.T., Heroux, A., Schlessman, J.L.

(2014) Proteins 82: 528-534

PubMed: 23999883 Search on PubMed
DOI: https://doi.org/10.1002/prot.24409
Primary Citation of Related Structures:
4L2M, 4MAX

PubMed Abstract:
The X-ray structures of the hemoglobin from Synechococcus sp. PCC 7002 (GlbN) were solved in the ferric bis-histidine (1.44 Å resolution) and cyanide-bound (2.25 Å resolution) states with covalently attached heme. The two structures illustrate the conformational changes and cavity opening caused by exogenous ligand binding. They also reveal an unusually distorted heme, ruffled as in c cytochromes. Comparison to the solution structure demonstrates the influence of crystal packing on several structural elements, whereas comparison to GlbN from Synechocystis sp. PCC 6803 shows subtle differences in heme geometries and environment. The new structures will be instrumental in elucidating GlbN reactivity.

Organizational Affiliation

T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, 21218.

Macromolecule Content

Total Structure Weight: 29.06 kDa
Atom Count: 2,076
Modelled Residue Count: 246
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanoglobin	A, B	123	Picosynechococcus sp. PCC 7002	Mutation(s): 0 Gene Names: glbN, SYNPCC7002_A1621
UniProt
Find proteins for Q8RT58 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)) Explore Q8RT58 Go to UniProtKB: Q8RT58
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RT58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEB Query on HEB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	HEME B/C C₃₄ H₃₄ Fe N₄ O₄ NEGHHAJBRZGUAY-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	E [auth A], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
CYN Query on CYN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.288
R-Value Work: 0.218
R-Value Observed: 0.221
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.622	α = 90
b = 40.951	β = 111.21
c = 66.461	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2013-06-19
Changes: Experimental preparation
Version 1.2: 2013-09-18
Changes: Database references
Version 1.3: 2014-02-19
Changes: Database references
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-20
Changes: Data collection, Structure summary