103M | pdb_0000103m

SPERM WHALE MYOGLOBIN H64A N-BUTYL ISOCYANIDE AT PH 9.0

PDB DOI: https://doi.org/10.2210/pdb103M/pdb

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

Deposited: 1997-12-16 Released: 1998-04-08
Deposition Author(s): Smith, R.D., Olson, J.S., Phillips Jr., G.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.216 (Depositor), 0.210 (DCC)
R-Value Work:
0.158 (Depositor), 0.150 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Correlations between Bound N-Alkyl Isocyanide Orientations and Pathways for Ligand Binding in Recombinant Myoglobins

(1999) Thesis

Macromolecule Content

Total Structure Weight: 18.09 kDa
Atom Count: 1,389
Modeled Residue Count: 154
Deposited Residue Count: 154
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	154	Physeter macrocephalus	Mutation(s): 2 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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NBN Query on NBN 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]	N-BUTYL ISOCYANIDE C₅ H₉ N FSBLVBBRXSCOKU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.216 (Depositor), 0.210 (DCC)
R-Value Work: 0.158 (Depositor), 0.150 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.63	α = 90
b = 91.63	β = 90
c = 46.014	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1998-04-08

Deposition Author(s):

Phillips Jr., G.N.

Revision History (Full details and data files)

Version 1.0: 1998-04-08
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-03-07
Changes: Data collection, Other
Version 1.4: 2021-11-03
Changes: Database references, Derived calculations
Version 1.5: 2024-02-07
Changes: Data collection
Version 1.6: 2024-04-03
Changes: Refinement description

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.