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- PDB-3dht: The Crystal Structure Determination of Rat (rattus norvegicus) He... -

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Basic information

Entry
Database: PDB / ID: 3dht
TitleThe Crystal Structure Determination of Rat (rattus norvegicus) Hemoglobin
Components
  • Hemoglobin subunit alpha-1/2
  • Hemoglobin subunit beta-1
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / Hemoglobin / heme / Iron / Metal-binding / Transport / Phosphoprotein
Function / homology
Function and homology information


hemoglobin beta binding / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Heme signaling / response to stilbenoid / Cytoprotection by HMOX1 / Neutrophil degranulation / nitric oxide transport / hemoglobin alpha binding ...hemoglobin beta binding / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Heme signaling / response to stilbenoid / Cytoprotection by HMOX1 / Neutrophil degranulation / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / erythrocyte development / hemoglobin complex / hemopoiesis / oxygen transport / 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-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
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: 2.98 Å
AuthorsNeelagandan, K. / Sathya Moorthy, P. / Balasubramanian, M. / Sundaresan, S. / Ponnuswamy, M.N.
Citation
Journal: To be Published
Title: The Crystal Structure Determination of Rat (rattus norvegicus) Hemoglobin
Authors: Neelagandan, K. / Sathya Moorthy, P. / Balasubramanian, M. / Sundaresan, S. / Ponnuswamy, M.N.
#1: Journal: Protein Pept.Lett. / Year: 2003
Title: Crystal structure of hemoglobin from the maned wolf (Chrysocyon brachyurus) using synchrotron radiation
Authors: Fadel, V. / Canduri, F. / Olivieri, J.R. / Smarra, A.L.S. / Colombo, M.F. / Bonilla-Rodriguez, G.O. / de Azevedo, W.F.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Derived calculations
Revision 1.3Dec 21, 2016Group: Other
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3294
Polymers31,0962
Non-polymers1,2332
Water23413
1
A: Hemoglobin subunit alpha-1/2
B: Hemoglobin subunit beta-1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)64,6578
Polymers62,1914
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)53.710, 53.710, 350.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Cell: red blood cell / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Cell: red blood cell / References: UniProt: P02091
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 13 / 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
Details: 40% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5478 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NIL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 2.97→30 Å / Num. all: 6233 / Num. obs: 6233 / Redundancy: 14.3 % / Rsym value: 0.2132 / Net I/σ(I): 3
Reflection shellResolution: 2.97→3.08 Å / Redundancy: 11.5 % / Rsym value: 0.3962

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
AUTOMARdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FHJ

1fhj


Resolution: 2.98→23.26 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.846 / SU B: 16.984 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.556 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27466 619 10 %RANDOM
Rwork0.23904 ---
obs0.24257 5596 90.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.98→23.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 86 13 2255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1252.0573156
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1745282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64824.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65215359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.414155
X-RAY DIFFRACTIONr_chiral_restr0.0790.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021743
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21034
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21559
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0220.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3711.51430
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5822238
X-RAY DIFFRACTIONr_scbond_it0.6863987
X-RAY DIFFRACTIONr_scangle_it0.9734.5914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.975→3.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 40 -
Rwork0.265 348 -
obs--83.62 %

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