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- PDB-5lfg: X-ray structure of a new fully ligated carbomonoxy form of Tremat... -

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Basic information

Entry
Database: PDB / ID: 5lfg
TitleX-ray structure of a new fully ligated carbomonoxy form of Trematomus newnesi hemoglobin (Hb1TnCO).
Components
  • Hemoglobin subunit alpha-1
  • Hemoglobin subunit beta-1/2
KeywordsOXYGEN TRANSPORT / globin fold
Function / homology
Function and homology information


haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-1 / Hemoglobin subunit beta-1/2
Similarity search - Component
Biological speciesTrematomus newnesi (dusky notothen)
MethodX-RAY DIFFRACTION / Resolution: 1.94 Å
AuthorsVitagliano, L. / Mazzarella, L. / Merlino, A. / Vergara, A.
CitationJournal: Chemistry / Year: 2017
Title: Fine Sampling of the RT Quaternary-Structure Transition of a Tetrameric Hemoglobin.
Authors: Vitagliano, L. / Mazzarella, L. / Merlino, A. / Vergara, A.
History
DepositionJul 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha-1
B: Hemoglobin subunit beta-1/2
C: Hemoglobin subunit alpha-1
D: Hemoglobin subunit beta-1/2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,47712
Polymers63,8994
Non-polymers2,5788
Water3,837213
1
A: Hemoglobin subunit alpha-1
B: Hemoglobin subunit beta-1/2
hetero molecules

A: Hemoglobin subunit alpha-1
B: Hemoglobin subunit beta-1/2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,47712
Polymers63,8994
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area12640 Å2
ΔGint-109 kcal/mol
Surface area23180 Å2
MethodPISA
2
C: Hemoglobin subunit alpha-1
D: Hemoglobin subunit beta-1/2
hetero molecules

C: Hemoglobin subunit alpha-1
D: Hemoglobin subunit beta-1/2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,47712
Polymers63,8994
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12090 Å2
ΔGint-116 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.206, 87.256, 109.648
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-355-

HOH

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Components

#1: Protein Hemoglobin subunit alpha-1 / / Alpha-1-globin / Hemoglobin alpha-1 chain


Mass: 15703.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus newnesi (dusky notothen) / References: UniProt: P45718
#2: Protein Hemoglobin subunit beta-1/2 / / Beta-1/2-globin / Hemoglobin beta-1/2 chain


Mass: 16246.427 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus newnesi (dusky notothen) / References: UniProt: P45720
#3: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 8
Details: Crystallization trials were performed under CO atmosphere. The dialysis technique was used to obtain protein crystals: the protein, in a 50 mM Tris pH 8.0 buffer with 2mM dithionite, with a ...Details: Crystallization trials were performed under CO atmosphere. The dialysis technique was used to obtain protein crystals: the protein, in a 50 mM Tris pH 8.0 buffer with 2mM dithionite, with a concentration of 5 mg x ml-1, was separated by the precipitant reservoir (2.0 M ammonium sulphate, 2 mM dithionite) via a dialysis membrane with a 8000 Da cutoff. Single crystals of the carbomonoxylated Hb1Tn (Hb1TnCO), suitable for X-ray diffraction, were grown in a week (size 0,2 x 0,2 x 0,1 mm3).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: Jul 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→8 Å / Num. obs: 55016 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 4
Reflection shellHighest resolution: 1.94 Å / Rmerge(I) obs: 0.4 / % possible all: 80.4

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Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementResolution: 1.94→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4479 -RANDOM
Rwork0.181 ---
obs--93.5 %-
Refinement stepCycle: 1 / Resolution: 1.94→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 180 213 4854

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