+Open data
-Basic information
Entry | Database: PDB / ID: 2xki | ||||||
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Title | Aquo-met structure of C.lacteus mini-Hb | ||||||
Components | NEURAL HEMOGLOBIN | ||||||
Keywords | OXYGEN STORAGE / METAL-BINDING | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | CEREBRATULUS LACTEUS (milky ribbon-worm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Pesce, A. / Nardini, M. / Dewilde, S. / Capece, L. / Marti, M.A. / Congia, S. / Salter, M.D. / Blouin, G.C. / Estrin, D.A. / Ascenzi, P. ...Pesce, A. / Nardini, M. / Dewilde, S. / Capece, L. / Marti, M.A. / Congia, S. / Salter, M.D. / Blouin, G.C. / Estrin, D.A. / Ascenzi, P. / Moens, L. / Bolognesi, M. / Olson, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Ligand Migration in the Apolar Tunnel of Cerebratulus Lacteus Mini-Hemoglobin. Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Capece, L. / Marti, M.A. / Congia, S. / Salter, M.D. / Blouin, G.C. / Estrin, D.A. / Ascenzi, P. / Moens, L. / Bolognesi, M. / Olson, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xki.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xki.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/2xki ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xki | HTTPS FTP |
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-Related structure data
Related structure data | 2xkgC 2xkhC 1kr7S 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
#1: Protein | Mass: 11546.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CEREBRATULUS LACTEUS (milky ribbon-worm) Tissue: NERVE TISSUE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O76242 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6 Details: 605 AMMONIUM SULPHATE, 50 MM SODIUM ACETATE PH 6.0, AT 4C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→35.09 Å / Num. obs: 27887 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KR7 Resolution: 1.3→35.09 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.224 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.346 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→35.09 Å
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Refine LS restraints |
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