9BKP

Crystal structure of rubredoxin from Pyrococcus furiosus reconstituted with FeCl3 solved by Fe/S-SAD

PDB DOI: https://doi.org/10.2210/pdb9BKP/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-29 Released: 2024-06-05
Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.185
R-Value Work: 0.155
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of rubredoxin from Pyrococcus furiosus reconstituted with FeCl3 solved by Fe/S-SAD

Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 6.09 kDa
Atom Count: 508
Modelled Residue Count: 53
Deposited Residue Count: 54
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A	54	Pyrococcus furiosus	Mutation(s): 0 Gene Names: rub, PF1282
UniProt
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P24297 Go to UniProtKB: P24297
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24297
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.185
R-Value Work: 0.155
R-Value Observed: 0.158
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.867	α = 90
b = 34.594	β = 90
c = 43.301	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-06-05
Type: Initial release

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 R01GM133198.