8VSH

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D

PDB DOI: https://doi.org/10.2210/pdb8VSH/pdb

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

Deposited: 2024-01-24 Released: 2024-04-03
Deposition Author(s): Lecomte, J.T.J., Martinez, J.E., Schlessman, J.L., Schultz, T.D., Siegler, M.A.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.226
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Heme D formation in a Shewanella benthica truncated hemoglobin

Lecomte, J.T.J., Martinez Grundman, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 53.88 kDa
Atom Count: 4,024
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): 2 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ADT Query on A1ADT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	{3-[(2R,5'R)-9',14'-diethenyl-5'-hydroxy-5',10',15',19'-tetramethyl-5-oxo-4,5-dihydro-3H-spiro[furan-2,4'-[21,22,23,24]tetraazapentacyclo[16.2.1.13,6.18,11.113,16]tetracosa[1,3(24),6,8,10,12,14,16(22),17,19]decaen]-20'-yl-kappa~4~N~21'~,N~22'~,N~23'~,N~24'~]propanoato}iron C₃₄ H₃₂ Fe N₄ O₅ CYBWRCIPTVPWKW-YDXXJHAFSA-M		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.226
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.364	α = 90
b = 104.604	β = 90
c = 150.71	γ = 90

Software Package:

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

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

8VSH

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D

Heme D formation in a Shewanella benthica truncated hemoglobin

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)