4F6D | pdb_00004f6d

Oxy structure of His100Phe Cerebratulus lacteus mini-hemoglobin

PDB DOI: https://doi.org/10.2210/pdb4F6D/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Cerebratulus lacteus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-05-14 Released: 2012-05-30
Deposition Author(s): Soman, J., Salter, M.D., Olson, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Oxy structure of His100Phe Cerebratulus lacteus mini-hemoglobin

Soman, J., Salter, M.D., Olson, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 12.2 kDa
Atom Count: 1,030
Modeled Residue Count: 110
Deposited Residue Count: 110
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neural hemoglobin	A	110	Cerebratulus lacteus	Mutation(s): 1
UniProt
Find proteins for O76242 (Cerebratulus lacteus) Explore O76242 Go to UniProtKB: O76242
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O76242
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]
OXY Query on OXY 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]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-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: 1.80 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.528	α = 90
b = 43.485	β = 90
c = 59.498	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-05-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-30
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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.