3NP0

Crystal Structure of Pd(allyl)/apo-E45C/H49A/R52H-rHLFr

PDB DOI: https://doi.org/10.2210/pdb3NP0/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Equus caballus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-06-27 Released: 2010-12-22
Deposition Author(s): Wang, Z., Ueno, T., Abe, S., Takezawa, Y., Aoyagi, H., Hikage, T., Watanabe, Y., Kitagawa, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.210
R-Value Work: 0.198
R-Value Observed: 0.199

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Definite coordination arrangement of organometallic palladium complexes accumulated on the designed interior surface of apo-ferritin.

Wang, Z., Takezawa, Y., Aoyagi, H., Abe, S., Hikage, T., Watanabe, Y., Kitagawa, S., Ueno, T.

(2011) Chem Commun (Camb) 47: 170-172

PubMed: 20730233 Search on PubMed
DOI: https://doi.org/10.1039/c0cc02221g
Primary Citation of Related Structures:
3NOZ, 3NP0, 3NP2

PubMed Abstract:
Apo-ferritin (apo-Fr) mutants are used as scaffolds to accommodate palladium (allyl) complexes. Various coordination arrangements of the Pd complexes are achieved by adjusting the positions of cysteine and histidine residues on the interior surface of the apo-Fr cage.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Nagoya, 464-8602, Japan.

Macromolecule Content

Total Structure Weight: 21.45 kDa
Atom Count: 1,687
Modelled Residue Count: 174
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): 3 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
PLL Query on PLL Download Ideal Coordinates CCD File SDF format, chain D [auth X] SDF format, chain E [auth X] SDF format, chain F [auth X] SDF format, chain G [auth X] SDF format, chain H [auth X] SDF format, chain I [auth X] MOL2 format, chain D [auth X] MOL2 format, chain E [auth X] MOL2 format, chain F [auth X] MOL2 format, chain G [auth X] MOL2 format, chain H [auth X] MOL2 format, chain I [auth X] mmCIF format, chain D [auth X] mmCIF format, chain E [auth X] mmCIF format, chain F [auth X] mmCIF format, chain G [auth X] mmCIF format, chain H [auth X] mmCIF format, chain I [auth X]	D [auth X] E [auth X] F [auth X] G [auth X] H [auth X] D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X]	Palladium(II) allyl complex C₃ H₅ Pd WTWGCTVOVPTEEU-UHFFFAOYSA-N		Interactions Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Interactions & Density Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain J [auth X] MOL2 format, chain J [auth X] mmCIF format, chain J [auth X]	J [auth X]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain J [auth X] Interactions & Density Focus chain J [auth X]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth X] SDF format, chain C [auth X] MOL2 format, chain B [auth X] MOL2 format, chain C [auth X] mmCIF format, chain B [auth X] mmCIF format, chain C [auth X]	B [auth X], C [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth X] Focus chain C [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth X] SDF format, chain L [auth X] SDF format, chain M [auth X] SDF format, chain N [auth X] SDF format, chain O [auth X] SDF format, chain P [auth X] SDF format, chain Q [auth X] SDF format, chain R [auth X] MOL2 format, chain K [auth X] MOL2 format, chain L [auth X] MOL2 format, chain M [auth X] MOL2 format, chain N [auth X] MOL2 format, chain O [auth X] MOL2 format, chain P [auth X] MOL2 format, chain Q [auth X] MOL2 format, chain R [auth X] mmCIF format, chain K [auth X] mmCIF format, chain L [auth X] mmCIF format, chain M [auth X] mmCIF format, chain N [auth X] mmCIF format, chain O [auth X] mmCIF format, chain P [auth X] mmCIF format, chain Q [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.210
R-Value Work: 0.198
R-Value Observed: 0.199
Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.959	α = 90
b = 180.959	β = 90
c = 180.959	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: 2010-12-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-22
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