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- PDB-3nfe: The crystal structure of hemoglobin I from trematomus newnesi in ... -

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Basic information

Entry
Database: PDB / ID: 3nfe
TitleThe crystal structure of hemoglobin I from trematomus newnesi in deoxygenated state
Components
  • Hemoglobin subunit alpha-1
  • Hemoglobin subunit beta-1/2
KeywordsOXYGEN TRANSPORT / root effect / fish hemoglobin / antarctic fish
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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-1 / Hemoglobin subunit beta-1/2
Similarity search - Component
Biological speciesTrematomus newnesi (dusky notothen)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsVergara, A. / Vitagliano, L. / Merlino, A. / Sica, F. / Marino, K. / Mazzarella, L.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: An order-disorder transition plays a role in switching off the root effect in fish hemoglobins.
Authors: Vergara, A. / Vitagliano, L. / Merlino, A. / Sica, F. / Marino, K. / Verde, C. / di Prisco, G. / Mazzarella, L.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)66,3658
Polymers63,8994
Non-polymers2,4664
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-104 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.022, 62.022, 187.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


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 / / Hemoglobin beta-1/2 chain / Beta-1/2-globin


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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6
Details: protein at 10 mg/ml, in 100 mM sodium acetate buffer pH 6.0, 2mM dithionite, poured into a capillary containing 20% (w/v) MPEG 5000 (2 mM dithionite), LIQUID DIFFUSION, temperature 298K

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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: Jan 1, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→39.7 Å / Num. obs: 42455

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Processing

Software
NameClassification
CrystalCleardata collection
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H8F

2h8f


Resolution: 2.01→39.7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: IN THE COURSE OF THE REFINEMENT (SEE BELOW), IT BECAME OBVIOUS THAT CRYSTALS WERE AFFECTED BY MEROHEDRAL TWINNING AND THE DIFFRACTION PATTERN WAS INTERPRETED AS RESULTING FROM TWO LATTICES ...Details: IN THE COURSE OF THE REFINEMENT (SEE BELOW), IT BECAME OBVIOUS THAT CRYSTALS WERE AFFECTED BY MEROHEDRAL TWINNING AND THE DIFFRACTION PATTERN WAS INTERPRETED AS RESULTING FROM TWO LATTICES CORRELATED BY ROTATION OF 180 AROUND AN AXIS PARALLEL TO A + B DIAGONAL. THEREFORE, THE INTENSITY ASSOCIATED TO EACH REFLECTION HKL IS THE WEIGHTED SUM OF TWO CONTRIBUTIONS: IO (HKL)= (1-C) I(HKL) + C I(KHL), C IS THE TWIN FRACTION, WHICH REFINED TO A VALUE OF 0.38
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2238 -RANDOM
Rwork0.185 ---
obs0.185 42455 90.6 %-
Refinement stepCycle: LAST / Resolution: 2.01→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 172 138 4804
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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