6KRF | pdb_00006krf

An X-ray structure of ferric F43Y/F46S sperm whale myoglobin in complex with guaiacol

PDB DOI: https://doi.org/10.2210/pdb6KRF/pdb

Classification: OXYGEN STORAGE
Organism(s): Physeter macrocephalus
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2019-08-21 Released: 2020-07-01
Deposition Author(s): Yuan, H., Lin, Y.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.205 (Depositor), 0.206 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A Catalytic Binding Site Together with a Distal Tyr in MyoglobinAffords Catalytic Efficiencies Similar to Natural Peroxidases.

Zhang, P., Yuan, H., Xu, J., Wang, X.J., Gao, S.Q., Tan, X., Lin, Y.W.

(2020) ACS Catal 10: 891-896

DOI: https://doi.org/10.1021/acscatal.9b05080

Macromolecule Content

Total Structure Weight: 17.93 kDa
Atom Count: 1,479
Modeled Residue Count: 153
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Physeter macrocephalus	Mutation(s): 2 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]
JZ3 (Subject of Investigation/LOI) Query on JZ3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Guaiacol C₇ H₈ O₂ LHGVFZTZFXWLCP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.205 (Depositor), 0.206 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.794	α = 90
b = 48.558	β = 90
c = 78.595	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.