3H7G | pdb_00003h7g

Apo-FR with AU ions

PDB DOI: https://doi.org/10.2210/pdb3H7G/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Equus caballus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-04-27 Released: 2009-09-15
Deposition Author(s): Abe, M., Ueno, T., Abe, S., Suzuki, M., Goto, T., Toda, Y., Akita, T., Yamada, Y., Watanabe, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.236 (Depositor), 0.230 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Preparation and catalytic reaction of Au/Pd bimetallic nanoparticles in apo-ferritin

Suzuki, M., Abe, M., Ueno, T., Abe, S., Goto, T., Toda, Y., Akita, T., Yamada, Y., Watanabe, Y.

(2009) Chem Commun (Camb) 32: 4871-4873

PubMed: 19652809 Search on PubMed
DOI: https://doi.org/10.1039/b908742g
Primary Citation of Related Structures:
3H7G

PubMed Abstract:
We have succeeded in preparing Au/Pd core-shell nanoparticles in apo-ferritin and improving the catalytic reactivity of olefin hydrogenation relative to Pd0 nanoparticles in the cage.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8020, Japan.

Macromolecule Content

Total Structure Weight: 22.03 kDa
Atom Count: 1,645
Modelled Residue Count: 173
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A	174	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791 Go to UniProtKB: P02791
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02791
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AU3 Query on AU3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GOLD 3+ ION Au CBMIPXHVOVTTTL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	K [auth A], L [auth A], M [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	N [auth A], O [auth A], P [auth A], Q [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.236 (Depositor), 0.230 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.632	α = 90
b = 181.632	β = 90
c = 181.632	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description