3PI4 | pdb_00003pi4

Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 4.0

PDB DOI: https://doi.org/10.2210/pdb3PI4/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Phacoides pectinatus
Mutation(s): Yes

Deposited: 2010-11-05 Released: 2011-11-09
Deposition Author(s): Gavira, J.A., Nieves-Marrero, C.A., Ruiz-Martinez, C.R., Estremera-Andujar, R.A., Lopez-Garriga, J., Garcia-Ruiz, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.17 Å
R-Value Free:
0.287 (Depositor), 0.275 (DCC)
R-Value Work:
0.196 (Depositor), 0.195 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

pH-dependence crystallographic studies of the oxygen carrier hemoglobin II from Lucina pectinata

Nieves-Marrero, C.A., Ruiz-Martinez, C.R., Estremera-Andujar, R.A., Lopez-Garriga, J., Garcia-Ruiz, J.M., Gavira, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 35.32 kDa
Atom Count: 2,452
Modeled Residue Count: 304
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin II	A, B	152	Phacoides pectinatus	Mutation(s): 1
UniProt
Find proteins for P41261 (Phacoides pectinatus) Explore P41261 Go to UniProtKB: P41261
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41261
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.17 Å
R-Value Free: 0.287 (Depositor), 0.275 (DCC)
R-Value Work: 0.196 (Depositor), 0.195 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.237	α = 90
b = 72.237	β = 90
c = 146.288	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Nieves-Marrero, C.A.

Ruiz-Martinez, C.R.

Estremera-Andujar, R.A.

Lopez-Garriga, J.

Garcia-Ruiz, J.M.

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.