3WR1 | pdb_00003wr1

Crystal structure of Cormorant (Phalacrocorax carbo) hemoglobin

PDB DOI: https://doi.org/10.2210/pdb3WR1/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Phalacrocorax carbo
Mutation(s): No

Deposited: 2014-02-09 Released: 2014-03-05
Deposition Author(s): Jagadeesan, G., Vinodh Kumar, V., Peters, H.G., Malathy, P., Harikrishna Etti, S., Gunasekaran, K., Aravindhan, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.188 (Depositor), 0.196 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Cormorant (Phalacrocorax carbo) hemoglobin

Jagadeesan, G., Vinodh Kumar, V., Peters, H.G., Malathy, P., Harikrishna Etti, S., Gunasekaran, K., Aravindhan, S.

To be published.

Macromolecule Content

Total Structure Weight: 32.66 kDa
Atom Count: 2,304
Modeled Residue Count: 287
Deposited Residue Count: 287
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-A	A	141	Phalacrocorax carbo	Mutation(s): 0
UniProt
Find proteins for P10780 (Phalacrocorax carbo) Explore P10780 Go to UniProtKB: P10780
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10780
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	146	Phalacrocorax carbo	Mutation(s): 0
UniProt
Find proteins for P10782 (Phalacrocorax carbo) Explore P10782 Go to UniProtKB: P10782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10782
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: 3.50 Å
R-Value Free: 0.265 (Depositor), 0.270 (DCC)
R-Value Work: 0.188 (Depositor), 0.196 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.64	α = 90
b = 55.64	β = 90
c = 153.381	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-03-05

Deposition Author(s):

Vinodh Kumar, V.

Harikrishna Etti, S.

Gunasekaran, K.

Revision History (Full details and data files)

Version 1.0: 2014-03-05
Type: Initial release
Version 1.1: 2014-06-25
Changes: Other
Version 1.2: 2014-07-02
Changes: Other
Version 1.3: 2021-09-15
Changes: Database references, Derived calculations
Version 1.4: 2023-11-08
Changes: Data collection, 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.