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), 0.215 (DCC)
R-Value Work:
0.169 (Depositor)
R-Value Observed:
0.172 (Depositor)

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.215 (DCC)
R-Value Work: 0.169 (Depositor)
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

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Ligand Structure Quality Assessment

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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

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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.