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- PDB-2h8f: Crystal structure of deoxy hemoglobin from Trematomus bernacchii ... -

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Basic information

Entry
Database: PDB / ID: 2h8f
TitleCrystal structure of deoxy hemoglobin from Trematomus bernacchii at pH 6.2
Components
  • Hemoglobin alpha subunit
  • Hemoglobin beta subunit
KeywordsTRANSPORT PROTEIN / Root effect / pH / cooperativity / hemoglobin / allostery / high resolution
Function / homology
Function and homology information


haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin 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 ...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 / Hemoglobin subunit beta
Similarity search - Component
Biological speciesTrematomus bernacchii (emerald rockcod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsMazzarella, L. / Vergara, A. / Vitagliano, L. / Merlino, A. / Bonomi, G. / Scala, S. / Verde, C. / di Prisco, G.
Citation
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.
#1: 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.
#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
DepositionJun 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 alpha subunit
B: Hemoglobin beta subunit
C: Hemoglobin alpha subunit
D: Hemoglobin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1398
Polymers63,6734
Non-polymers2,4664
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-104 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.850, 95.042, 61.824
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


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 beta subunit / Hemoglobin beta chain / Beta-globin


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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→19.83 Å / Num. all: 150761 / Num. obs: 150761 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.3→1.46 Å / % possible all: 57.2

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
SHELXL-97refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.3→19.83 Å / Stereochemistry target values: Engh & Huber
Details: Crystals used for structure determination present pseudo-merohedral twinning
RfactorNum. reflectionSelection details
Rfree0.172 7536 random
Rwork0.151 --
all0.156 150602 -
obs0.151 143066 -
Refinement stepCycle: LAST / Resolution: 1.3→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 172 511 5191
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d3

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