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- PDB-3d4x: Crystal structure determination of cat (Felis silvestris catus) h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d4x | ||||||
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Title | Crystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.2 angstrom resolution | ||||||
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![]() | Oxygen storage / Oxygen transport / Felis silvestris catus / Monoclinic / Hemoglobin / low oxygen affinity / allosteric mechanism / Heme / Iron / Transport | ||||||
Function / homology | ![]() hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N. | ||||||
![]() | ![]() Title: Crystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.2 angstrom resolution Authors: Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization of sheep (Ovis aries) and goat (Capra hircus) haemoglobins under unbuffered low-salt conditions Authors: Neelagandan, K. / Sathya Moorthy, P. / Balasubramanian, M. / Ponnuswamy, M.N. #2: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Purification, crystallization and preliminary crystallographic study of low oxygen-affinity haemoglobin from cat (Felis silvestris catus) in two different crystal forms Authors: Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N. #3: Journal: Protein Pept.Lett. / Year: 2009 Title: Preliminary Crystallographic Study of Hemoglobin from Buffalo (Bubalus bubalis): A Low Oxygen Affinity Species Authors: Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N. #4: ![]() Title: Purification, Crystallization and Preliminary X-Ray Diffraction Studies on Goat (Capra hircus) Hemoglobin - A Low Oxygen Affinity Species Authors: Sathya Moorthy, P. / Neelagandan, K. / Balasubramanian, M. / Ponnuswamy, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.1 KB | Display | ![]() |
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PDB format | ![]() | 99.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 34.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hdaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15328.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 15892.134 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 26, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 28427 / % possible obs: 95.2 % / Redundancy: 2.46 % / Rmerge(I) obs: 0.0685 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3036 / Mean I/σ(I) obs: 1.2 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HDA Resolution: 2.2→29.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.223 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.379 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.963 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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