2ZUR

Crystal Structure of Rh(nbd)/apo-Fr

PDB DOI: https://doi.org/10.2210/pdb2ZUR/pdb

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

Deposited: 2008-10-28 Released: 2009-06-02
Deposition Author(s): Abe, S., Hirata, K., Ueno, T., Shimizu, N., Yamamoto, M., Takata, M., Watanabe, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.196
R-Value Work: 0.175
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Polymerization of phenylacetylene by rhodium complexes within a discrete space of apo-ferritin

Abe, S., Hirata, K., Ueno, T., Morino, K., Shimizu, N., Yamamoto, M., Takata, M., Yashima, E., Watanabe, Y.

(2009) J Am Chem Soc 131: 6958-6960

PubMed: 19453195 Search on PubMed
DOI: https://doi.org/10.1021/ja901234j
Primary Citation of Related Structures:
2ZUR

PubMed Abstract:
Polymerization reactions of phenylacetylene derivatives are promoted by rhodium complexes within the discrete space of apo-ferritin in aqueous media. The catalytic reaction provides polymers with restricted molecular weight and a narrow molecular weight distribution. These results suggest that protein nanocages have potential for use as various reaction spaces through immobilization of metal catalysts on the interior surfaces of the protein cages.

Organizational Affiliation

Institute for Integrated Cell-Material Sciences, Funai Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.

Macromolecule Content

Total Structure Weight: 21.52 kDa
Atom Count: 1,710
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 [auth X]	174	Equus caballus	Mutation(s): 0 Gene Names: FTL
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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain E [auth X] SDF format, chain B [auth X] SDF format, chain D [auth X] SDF format, chain F [auth X] MOL2 format, chain C [auth X] MOL2 format, chain E [auth X] MOL2 format, chain B [auth X] MOL2 format, chain D [auth X] MOL2 format, chain F [auth X] mmCIF format, chain C [auth X] mmCIF format, chain E [auth X] mmCIF format, chain B [auth X] mmCIF format, chain D [auth X] mmCIF format, chain F [auth X]	B [auth X], C [auth X], D [auth X], E [auth X], F [auth X]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X]
RH Query on RH Download Ideal Coordinates CCD File SDF format, chain J [auth X] SDF format, chain I [auth X] MOL2 format, chain J [auth X] MOL2 format, chain I [auth X] mmCIF format, chain J [auth X] mmCIF format, chain I [auth X]	I [auth X], J [auth X]	Rhodium Rh OBDSITLACDGNMC-UHFFFAOYSA-N		Interactions Focus chain I [auth X] Focus chain J [auth X] Interactions & Density Focus chain I [auth X] Focus chain J [auth X]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth X] SDF format, chain H [auth X] MOL2 format, chain G [auth X] MOL2 format, chain H [auth X] mmCIF format, chain G [auth X] mmCIF format, chain H [auth X]	G [auth X], H [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth X] Focus chain H [auth X] Interactions & Density Focus chain G [auth X] Focus chain H [auth X]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth X] SDF format, chain M [auth X] SDF format, chain O [auth X] SDF format, chain P [auth X] SDF format, chain Q [auth X] SDF format, chain L [auth X] SDF format, chain N [auth X] SDF format, chain R [auth X] MOL2 format, chain K [auth X] MOL2 format, chain M [auth X] MOL2 format, chain O [auth X] MOL2 format, chain P [auth X] MOL2 format, chain Q [auth X] MOL2 format, chain L [auth X] MOL2 format, chain N [auth X] MOL2 format, chain R [auth X] mmCIF format, chain K [auth X] mmCIF format, chain M [auth X] mmCIF format, chain O [auth X] mmCIF format, chain P [auth X] mmCIF format, chain Q [auth X] mmCIF format, chain L [auth X] mmCIF format, chain N [auth X] mmCIF format, chain R [auth X]	K [auth X] L [auth X] M [auth X] N [auth X] O [auth X] K [auth X], L [auth X], M [auth X], N [auth X], O [auth X], P [auth X], Q [auth X], R [auth X]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Focus chain P [auth X] Focus chain Q [auth X] Focus chain R [auth X] Interactions & Density Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Focus chain P [auth X] Focus chain Q [auth X] Focus chain R [auth X]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
C4R Query on C4R	A [auth X]	L-PEPTIDE LINKING	C₁₀ H₁₄ N O₂ Rh S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.196
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.276	α = 90
b = 181.276	β = 90
c = 181.276	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-06-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-10-23
Changes: Structure summary