2VKR | pdb_00002vkr

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin

PDB DOI: https://doi.org/10.2210/pdb2VKR/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Acidianus ambivalens
Mutation(s): No

Deposited: 2007-12-23 Released: 2008-03-04
Deposition Author(s): Frazao, C., Aragao, D., Coelho, R., Leal, S.S., Gomes, C.M., Teixeira, M., Carrondo, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.273 (Depositor), 0.229 (DCC)
R-Value Work:
0.218 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.

Frazao, C., Aragao, D., Coelho, R., Leal, S.S., Gomes, C.M., Teixeira, M., Carrondo, M.A.

(2008) FEBS Lett 582: 763-767

PubMed: 18258200 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2008.01.041
Primary Citation Related Structures:
2VKR

PubMed Abstract:
Detailed structural models of di-cluster seven-iron ferredoxins constitute a valuable resource for folding and stability studies relating the metal cofactors' role in protein stability. The here reported, hemihedric twinned crystal structure at 2.0 A resolution from Acidianus ambivalens ferredoxin, shows an integral 103 residues, physiologically relevant native form composed by a N-terminal extension comprising a His/Asp Zn(2+) site and the ferredoxin (betaalphabeta)(2) core, which harbours intact clusters I and II, a [3Fe-4S](1+/0) and a [4Fe-4S](2+/1+) centres. This is in contrast with the previously available ferredoxin structure from Sulfolofus tokodai, which was obtained from an artificial oxidative conversion with two [3Fe-4S](1+/0) centres and poor definition around cluster II.

Organizational Affiliation

Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av da República, Oeiras, Portugal. frazao@itqb.unl.pt

Macromolecule Content

Total Structure Weight: 82.09 kDa
Atom Count: 5,616
Modeled Residue Count: 721
Deposited Residue Count: 721
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZINC-CONTAINING FERREDOXIN	A, B, C, D, E A, B, C, D, E, F, G	103	Acidianus ambivalens	Mutation(s): 0
UniProt
Find proteins for P49949 (Acidianus ambivalens) Explore P49949 Go to UniProtKB: P49949
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49949
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] SDF format, chain I [auth A] MOL2 format, chain AA [auth G] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth G] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F] mmCIF format, chain I [auth A]	AA [auth G] I [auth A] L [auth B] O [auth C] R [auth D] AA [auth G], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain H [auth A]	H [auth A] K [auth B] N [auth C] Q [auth D] T [auth E] H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], W [auth F], Z [auth G]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain BA [auth G] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain BA [auth G] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	BA [auth G] J [auth A] M [auth B] P [auth C] S [auth D] BA [auth G], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.273 (Depositor), 0.229 (DCC)
R-Value Work: 0.218 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.5	α = 90
b = 117.5	β = 90
c = 50.9	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-03-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-03-04
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-01-30
Changes: Data collection, Database references, Experimental preparation
Version 1.4: 2019-05-22
Changes: Data collection, Refinement description
Version 1.5: 2023-03-29
Changes: Database references, Derived calculations, Other, Structure summary
Version 1.6: 2024-02-07
Changes: Data collection, Refinement description

2VKR | pdb_00002vkr

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin

Literature

Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Biological Assembly 7

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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