3U9J | pdb_00003u9j

Crystal structure of oxidized human FBXL5 hemerythrin like domain

PDB DOI: https://doi.org/10.2210/pdb3U9J/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-19 Released: 2012-02-22
Deposition Author(s): Li, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.217 (Depositor), 0.216 (DCC)
R-Value Work:
0.167 (Depositor), 0.164 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3U9J

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

Literature

The Structural Basis of Iron Sensing by the Human F-box Protein FBXL5.

Shu, C., Sung, M.W., Stewart, M.D., Igumenova, T.I., Tan, X., Li, P.

(2012) Chembiochem 13: 788-791

PubMed: 22492618 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/cbic.201200043
Primary Citation Related Structures:
3U9J, 3U9M

Organizational Affiliation

Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA.

Macromolecule Content

Total Structure Weight: 39.34 kDa
Atom Count: 3,057
Modeled Residue Count: 314
Deposited Residue Count: 320
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box/LRR-repeat protein 5	A, B	160	Homo sapiens	Mutation(s): 0 Gene Names: FBXL5, FBL4, FBL5, FLR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKA1 (Homo sapiens) Explore Q9UKA1 Go to UniProtKB: Q9UKA1
PHAROS: Q9UKA1 GTEx: ENSG00000118564
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.217 (Depositor), 0.216 (DCC)
R-Value Work: 0.167 (Depositor), 0.164 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.082	α = 90
b = 77.343	β = 90
c = 78.19	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-22
Type: Initial release
Version 1.1: 2012-04-25
Changes: Database references
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, 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.