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Yorodumi- PDB-3vrf: The crystal structure of hemoglobin from woolly mammoth in the ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vrf | ||||||
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Title | The crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy forms | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / woolly mammoth hemoglobin / OXYGEN STORAGE/TRANSPORT | ||||||
Function / homology | Function and homology information 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 | Mammuthus primigenius (woolly mammoth) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Noguchi, H. / Campbell, K.L. / Ho, C. / Park, S.-Y. / Tame, J.R.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structures of haemoglobin from woolly mammoth in liganded and unliganded states. Authors: Noguchi, H. / Campbell, K.L. / Ho, C. / Unzai, S. / Park, S.-Y. / Tame, J.R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vrf.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vrf.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vrf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3vrf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3vrf_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3vrf_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/3vrf ftp://data.pdbj.org/pub/pdb/validation_reports/vr/3vrf | HTTPS FTP |
-Related structure data
Related structure data | 3vreC 3vrgC 2dn3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15540.505 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mammuthus primigenius (woolly mammoth) / Strain: SP1349 (KIA27805) / Gene: HBA-T2 / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: D3U1H8 | ||||
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#2: Protein | Mass: 16178.507 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mammuthus primigenius (woolly mammoth) / Strain: SP1349 (KIA27805) / Gene: HBB/D / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: D3U1H9 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 293 K / Method: batch / pH: 7.5 Details: Sodium/potassium phosphate, pH 7.5, BATCH, temperature 293K, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 17, 2010 / Details: Si(111) |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 47308 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 1.55→1.58 Å / Rmerge(I) obs: 0.187 / % possible all: 83.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DN3 Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.171 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.417 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.551→1.591 Å / Total num. of bins used: 20
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