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- PDB-3d1k: R/T intermediate quaternary structure of an antarctic fish hemogl... -

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Basic information

Entry
Database: PDB / ID: 3d1k
TitleR/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) state
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN BINDING / antarctic fish hemoglobin / intermediate R/T quaternary structure / oxidation pathway / Heme / Iron / Metal-binding / Oxygen transport / Transport / Acetylation
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / 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-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETYL GROUP / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-1 / Hemoglobin subunit beta-1/2
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsVitagliano, L. / Vergara, A. / Bonomi, G. / Merlino, A. / Mazzarella, L.
Citation
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.
#1: Journal: Proteins / Year: 2006
Title: High resolution crystal structure of deoxy hemoglobin from Trematomus bernacchii at different pH values: the role of histidine residues in modulating the strength of the root effect.
Authors: Mazzarella, L. / Vergara, A. / Vitagliano, L. / Merlino, A. / Bonomi, G. / Scala, S. / Verde, C. / di Prisco, G.
#2: Journal: Proteins / Year: 2006
Title: Minimal structural requirements for root effect: crystal structure of the cathodic hemoglobin isolated from the antarctic fish Trematomus newnesi.
Authors: Mazzarella, L. / Bonomi, G. / Lubrano, M.C. / Merlino, A. / Riccio, A. / Vergara, A. / Vitagliano, L. / Verde, C. / di Prisco, G.
History
DepositionMay 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / 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 / _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 subunit alpha-1
B: Hemoglobin subunit beta-1/2
A: ACETYL GROUP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2296
Polymers31,9242
Non-polymers1,3054
Water5,350297
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)66,45712
Polymers63,8474
Non-polymers2,6108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12110 Å2
ΔGint-105 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.458, 87.664, 55.502
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Hemoglobin subunit ... , 2 types, 2 molecules AB

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


Mass: 15677.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene HBA1 / Species: Trematomus newnesi / 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.: 1 / Source method: isolated from a natural source / Species: Trematomus newnesi / References: UniProt: P45720

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Non-polymers , 4 types, 301 molecules A

#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7.6
Details: Crysatls grew in a week by using a protein concentration of 6mg/ml and 14% w/v MPEG5000 in a 50mM Tris HCl buffer at 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
DetectorDetector: CCD / Date: Nov 4, 2000 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 114368

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T1N

1t1n


Resolution: 1.25→30 Å / Cross valid method: troughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 --RANDOM
Rwork0.167 ---
obs0.167 114368 99.6 %-
all-114368 --
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 91 297 2658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTION1-2 distances0.019
X-RAY DIFFRACTION1-3 distances0.038
LS refinement shellResolution: 1.25→1.29 Å / % reflection obs: 99.4 %

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