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- PDB-4iro: Crystal structure of T-state carbonmonoxy hemoglobin from Tremato... -

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Basic information

Entry
Database: PDB / ID: 4iro
TitleCrystal structure of T-state carbonmonoxy hemoglobin from Trematomus bernacchii at pH 8.4
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Globin fold
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesTrematomus bernacchii (emerald rockcod)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsMerlino, A. / Balsamo, A. / Mazzarella, L. / Vergara, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Role of tertiary structures on the Root effect in fish hemoglobins.
Authors: Ronda, L. / Merlino, A. / Bettati, S. / Verde, C. / Balsamo, A. / Mazzarella, L. / Mozzarelli, A. / Vergara, A.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1679
Polymers63,6734
Non-polymers2,4945
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-99 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.538, 104.802, 61.616
Angle α, β, γ (deg.)90.00, 90.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


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 subunit beta / Beta-globin / Hemoglobin beta chain


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-CMO / CARBON MONOXIDE


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


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


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: deoxy-HbTb crystals have been grown using 8-9.5 mg/ml protein mixed with equal amount of 7-12 % w/v PEG 6000, PBS 100 mM, KCl 0.3 M, pH 8.4. Deoxy HbTb crystals were then soaked for several ...Details: deoxy-HbTb crystals have been grown using 8-9.5 mg/ml protein mixed with equal amount of 7-12 % w/v PEG 6000, PBS 100 mM, KCl 0.3 M, pH 8.4. Deoxy HbTb crystals were then soaked for several hours in a deoxygenated, CO saturated, stabilizing solution containing 30% w/v PEG 6000, 100 mM Trsi-HCl pH 8.4, 200 mM KCl, 5 mM dithionite reducing agent and flushed with gaseous CO before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 27, 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: 2.2→72.165 Å / Num. all: 34835 / Num. obs: 34835

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Processing

Software
NameClassification
HKL-2000data collection
SHELXL-97model building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXL-97phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→72.165 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: DIFFRACTION DATA WERE COLLEXCTED ON TWO SINGLE CRYSTALS. THE TWO DATA SET WERE INDEXED, PROCESSED AND SCALED WITH HKL2000. THE AGREEMENT BETWEEN THE TWO DATA SETS WAS OF THE ORDER OF THE ...Details: DIFFRACTION DATA WERE COLLEXCTED ON TWO SINGLE CRYSTALS. THE TWO DATA SET WERE INDEXED, PROCESSED AND SCALED WITH HKL2000. THE AGREEMENT BETWEEN THE TWO DATA SETS WAS OF THE ORDER OF THE EXPECTED ERRORS (RMERGE 0.069). FOR EACH DATA SET, THE STRUCTURE WAS REFINED WITH SHELX PROGRAM. SINCE ALL THE BASIC FEATURES, SUCH AS THE COORDINATION AT THE HEME IRONS, SUBSTANTIALLY AGREE IN THE TWO STRUCTURES THE TWO DATA SETS WERE MERGED FOR SUCCESSIVE REFINEMENT STEPS. ALL REFLECTION WERE USED FOR REFINEMENT
RfactorNum. reflectionSelection details
Rwork0.219 --
obs0.22 33316 -
Rfree-1519 RANDOM
all-34835 -
Refinement stepCycle: LAST / Resolution: 2.2→72.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 174 37 4695

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