3O89 | pdb_00003o89

Crystal Structure of Sperm Whale Myoglobin G65T

PDB DOI: https://doi.org/10.2210/pdb3O89/pdb

Classification: OXYGEN STORAGE
Organism(s): Physeter macrocephalus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-08-02 Released: 2011-12-07
Deposition Author(s): Huang, X., Lovelace, L., Lebioda, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.183 (Depositor), 0.185 (DCC)
R-Value Work:
0.172 (Depositor)
R-Value Observed:
0.173 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Investigations of Structural Factors that Influence the Mechanism of Halophenol Dehalogenation using 'Peroxidase-Like' Myoglobin mutants and 'Myoglobin-Like' Amphitrite ornata Dehaloperoxidase Mutants

Huang, X., Du, J., Dawson, J., Lebioda, L.

To be published.

Macromolecule Content

Total Structure Weight: 18.09 kDa
Atom Count: 1,515
Modeled Residue Count: 153
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Physeter macrocephalus	Mutation(s): 1 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.183 (Depositor), 0.185 (DCC)
R-Value Work: 0.172 (Depositor)
R-Value Observed: 0.173 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.439	α = 90
b = 90.439	β = 90
c = 45.247	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-12-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-07
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.