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- PDB-4g51: Crystallographic analysis of the interaction of nitric oxide with... -

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Basic information

Entry
Database: PDB / ID: 4g51
TitleCrystallographic analysis of the interaction of nitric oxide with hemoglobin from Trematomus bernacchii in the T quaternary structure (fully ligated state).
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / All alpha proteins / oxygen transporter / N-terminal acetylated serine
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 / NITRIC OXIDE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesTrematomus bernacchii (emerald rockcod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsMerlino, A. / Balsamo, A. / Pica, A. / Mazzarella, L. / Vergara, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Selective X-ray-induced NO photodissociation in haemoglobin crystals: evidence from a Raman-assisted crystallographic study.
Authors: Merlino, A. / Fuchs, M.R. / Pica, A. / Balsamo, A. / Dworkowski, F.S. / Pompidor, G. / Mazzarella, L. / Vergara, A.
History
DepositionJul 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_reflns_twin / struct_conn
Item: _pdbx_reflns_twin.diffrn_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25912
Polymers63,6734
Non-polymers2,5868
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-110 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.002, 94.672, 61.956
Angle α, β, γ (deg.)90.00, 89.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


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


Mass: 16153.368 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80044
#3: Chemical
ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 298 K / pH: 6.2
Details: deoxy-HbTb 8-9.5 mg/ml mixed with equal amount of 7-12 % w/v PEG 6000, PBS 100 mM, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
merohedral11H,K,L10.398
merohedral11L,-K,H20.507
merohedral11-h,-k,l30.046
merohedral11L,K,-H40.049
ReflectionResolution: 2.27→50 Å / Num. obs: 26655 / % possible obs: 83.6 % / Observed criterion σ(I): 15.6 / Redundancy: 3.9 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 9.5 / % possible all: 56.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
SHELXL-97refinement
RefinementResolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 0.5
RfactorNum. reflection
Rfree0.249 1095
Rwork0.181 -
obs0.181 21249
all-21249
Displacement parametersBiso mean: 33.503 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 180 63 4725

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