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- PDB-3gkv: X-ray structure of an intermediate along the oxidation pathway of... -

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Basic information

Entry
Database: PDB / ID: 3gkv
TitleX-ray structure of an intermediate along the oxidation pathway of Trematomus bernacchii hemoglobin
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / hemoglobin / intermediate quaternary structure / Acetylation / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding ...haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / 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 / Hemoglobin subunit beta
Similarity search - Component
Biological speciesTrematomus bernacchii (emerald rockcod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMerlino, A. / Vitagliano, L. / Sica, F. / Vergara, A. / Mazzarella, L.
Citation
Journal: Biopolymers / Year: 2009
Title: Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins
Authors: Merlino, A. / Vitagliano, L. / Howes, B.D. / Verde, C. / di Prisco, G. / Smulevich, G. / Sica, F. / Vergara, A.
#1: Journal: J.Am.Chem.Soc. / Year: 2008
Title: Spectroscopic and crystallographic characterization of a tetrameric hemoglobin oxidation reveals structural features of the functional intermediate relaxed/tense state
Authors: Vitagliano, L. / Vergara, A. / Bonomi, G. / Merlino, A. / Verde, C. / di Prisco, G. / Howes, B.D. / Smulevich, G. / Mazzarella, L.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1266
Polymers31,8372
Non-polymers1,2894
Water4,342241
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)66,25112
Polymers63,6734
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13040 Å2
ΔGint-111 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.880, 87.647, 55.339
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


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 subunit beta / / Hemoglobin beta chain / Beta-globin


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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7.6
Details: protein concentration of 6mg/ml, 14% Mpeg 5000 in 50mM Tris/HCl buffer ph 7.6, LIQUID DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 80090 / % possible obs: 99.9 % / Rmerge(I) obs: 0.038

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PEG

2peg


Resolution: 1.4→28.25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.211 -RANDOM
Rwork0.184 --
all0.191 75819 -
obs0.184 75819 -
Refinement stepCycle: LAST / Resolution: 1.4→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 90 241 2636

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