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- PDB-1la6: The crystal structure of Trematomus newnesi hemoglobin in a parti... -

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Basic information

Entry
Database: PDB / ID: 1la6
TitleThe crystal structure of Trematomus newnesi hemoglobin in a partial hemichrome state
Components
  • Hemoglobin alpha-1 chain
  • Hemoglobin beta-1/2 chain
KeywordsOXYGEN STORAGE/TRANSPORT / Hemichrome / bishistidine complex / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRiccio, A. / Vitagliano, L. / di Prisco, G. / Zagari, A. / Mazzarella, L.
Citation
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.
#1: Journal: Acta Crystallogr. / Year: 2001
Title: Liganded and unliganded forms of Antarctic fish haemoglobins in polyethylene glycol: crystallization of an R-state haemichrome intermediate
Authors: Riccio, A. / Vitagliano, L. / di Prisco, G. / Zagari, A. / Mazzarella, L.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of Trematomus newnesi haemoglobin re-opens the root effect question
Authors: Mazzarella, L. / D'Avino, R. / di PRISCO, G. / Savino, C. / VITAGLIANO, L. / MOODY, P.C.E. / ZAGARI, A.
History
DepositionMar 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn_type / 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_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.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_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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 alpha-1 chain
B: Hemoglobin beta-1/2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2115
Polymers31,9502
Non-polymers1,2613
Water1,24369
1
A: Hemoglobin alpha-1 chain
B: Hemoglobin beta-1/2 chain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)66,42110
Polymers63,8994
Non-polymers2,5226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)89.853, 88.190, 55.142
Angle α, β, γ (deg.)90.00, 97.79, 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 operation: -X, Y, -Z

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Components

#1: Protein Hemoglobin alpha-1 chain


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


Mass: 16246.427 Da / Num. of mol.: 1 / 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


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


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 293 K / Method: free interface diffusion / pH: 7.6
Details: MPEG 5000, Sodium Acetate, pH 7.6, Free interface diffusion, temperature 293K
Crystal grow
*PLUS
pH: 6.2 / Details: Riccio, A., (2001) Acta Crystallogr., 57, 1144.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein11
2100 mMsodium acetate12pH6.2
310 %(w/v)MPEG500013

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 30, 2000 / 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→12 Å / Num. all: 27020 / Num. obs: 27020 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.077
Reflection shellResolution: 2→2.15 Å / Rmerge(I) obs: 0.35 / % possible all: 87
Reflection
*PLUS
% possible obs: 92 % / Num. measured all: 64025 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T1N

1t1n


Resolution: 2→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.212 2280 RANDOM
Rwork0.179 --
all0.191 26685 -
obs0.181 23191 -
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 88 71 2313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_dihedral_angle_d19.7
X-RAY DIFFRACTIONx_improper_angle_d1.44
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.191 / Rfactor obs: 0.181 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.44

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