8UZU

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin L80A C51S C71S variant

PDB DOI: https://doi.org/10.2210/pdb8UZU/pdb

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

Deposited: 2023-11-16 Released: 2024-04-03
Deposition Author(s): Schultz, T.D., Martinez, J.E., Siegler, M.A., Schlessman, J.L., Lecomte, J.T.J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224
R-Value Work: 0.195
R-Value Observed: 0.197

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 L80A C51S C71S variant

Schultz, T.D., Martinez, J.E., Siegler, M.A., Schlessman, J.L., Lecomte, J.T.J.

To be published.

Macromolecule Content

Total Structure Weight: 53.76 kDa
Atom Count: 4,282
Modelled Residue Count: 464
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224
R-Value Work: 0.195
R-Value Observed: 0.197
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.157	α = 90
b = 105.221	β = 90
c = 151.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data scaling
PHASER	phasing
CrysalisPro	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1330488
National Science Foundation (NSF, United States)	United States	CHE-2003950
National Science Foundation (NSF, United States)	United States	GRFP-1746891

Revision History (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

8UZU

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin L80A C51S C71S variant

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin L80A C51S C71S variant

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)