2Z6S

Crystal structure of the oxy myoglobin free from X-ray-induced photoreduction

PDB DOI: https://doi.org/10.2210/pdb2Z6S/pdb

Classification: OXYGEN BINDING
Organism(s): Physeter macrocephalus
Mutation(s): No

Deposited: 2007-08-08 Released: 2007-11-06
Deposition Author(s): Unno, M., Kusama, S., Chen, H., Shaik, S., Ikeda-Saito, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.187
R-Value Work: 0.136
R-Value Observed: 0.187

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structural Characterization of the Fleeting Ferric Peroxo Species in Myoglobin: Experiment and Theory

Unno, M., Chen, H., Kusama, S., Shaik, S., Ikeda-Saito, M.

(2007) J Am Chem Soc 129: 13394-13395

PubMed: 17929929 Search on PubMed
DOI: https://doi.org/10.1021/ja076108x
Primary Citation of Related Structures:
2Z6S, 2Z6T

Organizational Affiliation

Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan.

Macromolecule Content

Total Structure Weight: 18.08 kDa
Atom Count: 1,529
Modelled Residue Count: 152
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Physeter macrocephalus	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [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]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.187
R-Value Work: 0.136
R-Value Observed: 0.187
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.338	α = 90
b = 30.699	β = 105.46
c = 63.674	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-11-06
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

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Help and Resources

2Z6S

Crystal structure of the oxy myoglobin free from X-ray-induced photoreduction

Structural Characterization of the Fleeting Ferric Peroxo Species in Myoglobin: Experiment and Theory

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)