+Open data
-Basic information
Entry | Database: PDB / ID: 2xkh | ||||||
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Title | Xe derivative of C.lacteus mini-Hb Leu86Ala mutant | ||||||
Components | NEURAL HEMOGLOBIN | ||||||
Keywords | OXYGEN STORAGE / OXYGEN TRANSPORT / XE DERIVATIVE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.31 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 | 2xkh.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xkh.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xkh_validation.pdf.gz | 812.5 KB | Display | wwPDB validaton report |
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Full document | 2xkh_full_validation.pdf.gz | 813.9 KB | Display | |
Data in XML | 2xkh_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 2xkh_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/2xkh ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xkh | HTTPS FTP |
-Related structure data
Related structure data | 2xkgC 2xkiC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11504.869 Da / Num. of mol.: 1 / Mutation: YES 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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-Non-polymers , 5 types, 66 molecules
#2: Chemical | ChemComp-HEM / | ||
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#3: Chemical | ChemComp-OXY / | ||
#4: Chemical | ChemComp-SO4 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEEREDSequence details | UNP LEU87 HAS BEEN MUTATED TO ALA (RESIDUE 86 IN COORDINATE | |
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-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 / pH: 6 Details: 60% AMMONIUM SULPHATE, 50MM SODIUM ACETATE PH 6.0, AT 4C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35 Å / Num. obs: 5031 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.4 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KR7 Resolution: 2.31→18.29 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.869 / SU B: 8.313 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.29 / 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: 16.631 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→18.29 Å
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Refine LS restraints |
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