5V8S | pdb_00005v8s

Flavo di-iron protein H90D mutant from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb5V8S/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-22 Released: 2017-04-19 
• Deposition Author(s): Taylor, A.B., Becker, A., Giri, N., Hart, P.J., Kurtz Jr., D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Flavo Di-iron protein H90D Mutant from Thermotoga Maritima

Kurtz Jr., D.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.26 kDa 
• Atom Count: 7,028 
• Modeled Residue Count: 795 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavoprotein	A, B	410	Thermotoga maritima MSB8	Mutation(s): 1  Gene Names: TM_0755, Tmari_0756
UniProt
Find proteins for Q9WZL4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZL4  Go to UniProtKB:  Q9WZL4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FEO	C [auth A], H [auth B]	MU-OXO-DIIRON Fe2 O NPMYUMBHPJGBFA-UHFFFAOYSA-N
MRD	F [auth A], K [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
ACT	E [auth A], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A], G [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.616	α = 90
b = 91.857	β = 96.2
c = 85.479	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Taylor, A.B., Becker, A., Giri, N., Hart, P.J., Kurtz Jr., D.M.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-12-25
  Changes: Derived calculations, Structure summary