5MAB | pdb_00005mab

FoxE P3121 crystal structure of Rhodopseudomonas ferrooxidans SW2 putative iron oxidase

PDB DOI: https://doi.org/10.2210/pdb5MAB/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Rhodobacter ferrooxidans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-03 Released: 2017-12-20
Deposition Author(s): Pereira, L., Saraiva, I.H., Oliveira, A.S., Soares, C., Gomes, R.O., Frazao, C.
Funding Organization(s): FCT, MOSTMICRO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.169 (Depositor), 0.165 (DCC)
R-Value Work:
0.169 (Depositor), 0.168 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

FoxE P3121 crystal structure of Rhodopseudomonas ferrooxidans SW2 putative iron oxidase

Pereira, L., Saraiva, I.H., Coelho, R.

To be published.

Macromolecule Content

Total Structure Weight: 99.24 kDa
Atom Count: 6,349
Modeled Residue Count: 775
Deposited Residue Count: 873
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FoxE	A, B, C	291	Rhodobacter ferrooxidans	Mutation(s): 0 Gene Names: foxE
UniProt
Find proteins for A3DTD8 (Rhodobacter ferrooxidans) Explore A3DTD8 Go to UniProtKB: A3DTD8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3DTD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] H [auth B] I [auth B] M [auth C] D [auth A], E [auth A], H [auth B], I [auth B], M [auth C], N [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] J [auth B] K [auth B] O [auth C] F [auth A], G [auth A], J [auth B], K [auth B], O [auth C], P [auth C], Q [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.169 (Depositor), 0.165 (DCC)
R-Value Work: 0.169 (Depositor), 0.168 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.77	α = 90
b = 112.77	β = 90
c = 143.54	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
FCT	Portugal	SFRH/BPD/84404/2012
MOSTMICRO	Portugal	Lisboa-01-0145-FEDER-007660

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary