8VIJ

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin Y34F C51S C71S variant (cyanomet)

PDB DOI: https://doi.org/10.2210/pdb8VIJ/pdb

Classification: HEME-BINDING PROTEIN
Organism(s): Shewanella benthica KT99
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-01-04 Released: 2024-04-03
Deposition Author(s): Lecomte, J.T.J., Schlessman, J.L., Martinez, J.E., Schultz, T.D., Siegler, M.A., DelCampo, M., Le Magueres, P.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.201
R-Value Work: 0.163
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin Y34F C51S C71S variant in the cyanomet state

Lecomte, J.T.J.

To be published.

Macromolecule Content

Total Structure Weight: 53.86 kDa
Atom Count: 4,529
Modelled Residue Count: 464
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Group 1 truncated hemoglobin	A, B, C, D	116	Shewanella benthica KT99	Mutation(s): 3 Gene Names: KT99_16901
UniProt
Find proteins for A9DF82 (Shewanella benthica KT99) Explore A9DF82 Go to UniProtKB: A9DF82
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9DF82
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
CYN Query on CYN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]