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- PDB-1s5x: The crystal structure of Trematomus bernacchii hemoglobin oxidize... -

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Basic information

Entry
Database: PDB / ID: 1s5x
TitleThe crystal structure of Trematomus bernacchii hemoglobin oxidized by air
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / Hemichrome / bis-histidine / oxidation / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesTrematomus bernacchii (emerald rockcod)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVitagliano, L. / Bonomi, G. / Riccio, A. / di Prisco, G. / Smulevich, G. / Mazzarella, L.
Citation
Journal: Eur.J.Biochem. / Year: 2004
Title: The oxidation process of Antarctic fish hemoglobins
Authors: Vitagliano, L. / Bonomi, G. / Riccio, A. / Di Prisco, G. / Smulevich, G. / Mazzarella, L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The crystal structure of a tetrameric hemoglobin in a partial hemichrome state
Authors: Riccio, A. / Vitagliano, L. / di Prisco, G. / Zagari, A. / Mazzarella, L.
History
DepositionJan 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin alpha chain
B: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0704
Polymers31,8372
Non-polymers1,2332
Water48627
1
A: Hemoglobin alpha chain
B: Hemoglobin beta chain
hetero molecules

A: Hemoglobin alpha chain
B: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1398
Polymers63,6734
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)108.516, 65.095, 55.750
Angle α, β, γ (deg.)90.00, 113.48, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -X,Y,-Z

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Components

#1: Protein Hemoglobin alpha chain


Mass: 15683.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80043
#2: Protein Hemoglobin beta chain


Mass: 16153.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80044
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 7.6
Details: MPEG 5000, Tris, pH 7.6, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Jul 2, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 14020 / Num. obs: 14020 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.346 / % possible all: 99.6

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Processing

Software
NameClassification
XPRESSdata collection
DENZOdata reduction
AMoREphasing
CNSrefinement
XPRESSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.233 1087 RANDOM
Rwork0.19 --
all0.201 13525 -
obs0.195 12438 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 86 27 2267
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_improper_angle_d0.93

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