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- PDB-3hf4: Crystal structure of rat methemoglobin in R2 state -

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Basic information

Entry
Database: PDB / ID: 3hf4
TitleCrystal structure of rat methemoglobin in R2 state
Components
  • Hemoglobin subunit alpha-1/2
  • Hemoglobin subunit beta-1
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / Hemoglobin / quaternary structure / heme / Rattus norvegicus / Iron / Metal-binding / Polymorphism / Transport / Phosphoprotein
Function / homology
Function and homology information


Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Heme signaling / hemoglobin beta binding / regulation of eIF2 alpha phosphorylation by heme / response to stilbenoid / cellular oxidant detoxification / Cytoprotection by HMOX1 / nitric oxide transport ...Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Heme signaling / hemoglobin beta binding / regulation of eIF2 alpha phosphorylation by heme / response to stilbenoid / cellular oxidant detoxification / Cytoprotection by HMOX1 / nitric oxide transport / Neutrophil degranulation / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / hemopoiesis / erythrocyte development / negative regulation of blood pressure / glutathione metabolic process / hydrogen peroxide catabolic process / oxygen carrier activity / response to bacterium / carbon dioxide transport / response to hydrogen peroxide / oxygen binding / amyloid-beta binding / in utero embryonic development / iron ion binding / heme binding / protein-containing complex binding / extracellular space / 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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-1/2 / Hemoglobin subunit beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNeelagandan, K. / Sathya Moorthy, P. / Balasubramanian, M. / Ponnuswamy, M.N.
CitationJournal: To be Published
Title: Quaternary structural variability in rat hemoglobin
Authors: Neelagandan, K. / Sathya Moorthy, P. / Balasubramanian, M. / Ponnuswamy, M.N.
History
DepositionMay 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Jun 20, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Jan 15, 2020Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.6Nov 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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-1/2
B: Hemoglobin subunit beta-1
E: Hemoglobin subunit alpha-1/2
F: Hemoglobin subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6578
Polymers62,1914
Non-polymers2,4664
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11090 Å2
ΔGint-109 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.140, 54.015, 115.008
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemoglobin subunit alpha-1/2 / Hemoglobin alpha-1/2 chain / Alpha-1/2-globin


Mass: 15222.358 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Cell: blood plasma / Tissue: blood / References: UniProt: P01946
#2: Protein Hemoglobin subunit beta-1 / Hemoglobin beta-1 chain / Beta-1-globin / Hemoglobin beta chain / major-form


Mass: 15873.204 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Cell: blood plasma / Tissue: blood / References: UniProt: P02091
#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.: 14 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM phosphate buffer, peg 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 15682 / % possible obs: 97.4 % / Redundancy: 2.83 % / Rsym value: 0.1262 / Net I/σ(I): 4.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.68 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 1549 / Rsym value: 0.3198 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345researchdata collection
MOLREPphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3dht

3dht


Resolution: 2.7→19.16 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.828 / SU B: 15.879 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27497 1559 10 %RANDOM
Rwork0.21301 ---
obs0.21906 14091 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.491 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 172 14 4554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214677
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0282.0556391
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7825569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08624.108185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00215727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.431512
X-RAY DIFFRACTIONr_chiral_restr0.150.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.22014
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2870.23182
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2391.52886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43524516
X-RAY DIFFRACTIONr_scbond_it0.3932006
X-RAY DIFFRACTIONr_scangle_it0.6484.51867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 113 -
Rwork0.266 1013 -
obs--98.95 %

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