3ASE | pdb_00003ase

Crystal Structure of Zinc myoglobin soaked with Ru3O cluster

PDB DOI: https://doi.org/10.2210/pdb3ASE/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Physeter macrocephalus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-11 Released: 2011-04-27
Deposition Author(s): Koshiyama, T., Shirai, M., Hikage, T., Tabe, H., Tanaka, K., Kitagawa, S., Ueno, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.201 (Depositor), 0.198 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Post-Crystal Engineering of Zinc-Substituted Myoglobin to Construct a Long-Lived Photoinduced Charge-Separation System

Koshiyama, T., Shirai, M., Hikage, T., Tabe, H., Tanaka, K., Kitagawa, S., Ueno, T.

(2011) Angew Chem Int Ed Engl

PubMed: 21495132 Search on PubMed
DOI: https://doi.org/10.1002/anie.201008004
Primary Citation Related Structures:
3ASE

Organizational Affiliation

Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University iCeMS Lab Funai Center, Kyoto University Katsura, Kyoto 615-8510, Japan.

Macromolecule Content

Total Structure Weight: 18.82 kDa
Atom Count: 1,353
Modeled Residue Count: 154
Deposited Residue Count: 154
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 0 Gene Names: MB EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185 Go to UniProtKB: P02185
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZNH Query on ZNH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PROTOPORPHYRIN IX CONTAINING ZN C₃₄ H₃₂ N₄ O₄ Zn FUTVBRXUIKZACV-RGGAHWMASA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
RUO Query on RUO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	oxo-centered triruthenium cluster O Ru₃ VRRCAPVAMMGJAC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.201 (Depositor), 0.198 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.722	α = 90
b = 90.722	β = 90
c = 45.395	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations