2Z8Q | pdb_00002z8q

ferredoxin from Pyrococcus furiosus, D14C variant

PDB DOI: https://doi.org/10.2210/pdb2Z8Q/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Pyrococcus furiosus DSM 3638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-09-07 Released: 2007-09-18
Deposition Author(s): Johannessen, M.N., Christensen, H.E.M., Harris, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.194 (Depositor), 0.189 (DCC)
R-Value Work:
0.164 (Depositor), 0.162 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2Z8Q

This is version 1.5 of the entry. See complete history.

Literature

The crystal structure of the all cysteinyl coordinated D14C variant of [4Fe-4S] Pyrococcus furiosus ferredoxin

Johannessen, M.N., Nielsen, M.S., Ooi, B.L., Christensen, H.E.M., Harris, P.

To be published.

Macromolecule Content

Total Structure Weight: 15.67 kDa
Atom Count: 1,248
Modeled Residue Count: 132
Deposited Residue Count: 132
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin	A, B	66	Pyrococcus furiosus DSM 3638	Mutation(s): 1 Gene Names: fdxA
UniProt
Find proteins for P29603 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P29603 Go to UniProtKB: P29603
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29603
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
NCO Query on NCO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	D [auth A], E [auth A], G [auth B], H [auth B]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.194 (Depositor), 0.189 (DCC)
R-Value Work: 0.164 (Depositor), 0.162 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.4	α = 90
b = 116.8	β = 90
c = 47.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-09-18

Deposition Author(s):

Johannessen, M.N.

Christensen, H.E.M.

Revision History (Full details and data files)

Version 1.0: 2007-09-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-05-23
Changes: Atomic model
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description
Version 1.5: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.