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.

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
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Flavo Di-iron protein H90D Mutant from Thermotoga Maritima

Kurtz Jr., D.M.

To be published.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FEO Query on FEO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	MU-OXO-DIIRON Fe₂ O NPMYUMBHPJGBFA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A], G [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain I [auth B]

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-04-19

Deposition Author(s):

Revision History (Full details and data files)

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

5V8S | pdb_00005v8s

Flavo di-iron protein H90D mutant from Thermotoga maritima

Literature

Flavo Di-iron protein H90D Mutant from Thermotoga Maritima

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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