+Open data
-Basic information
Entry | Database: PDB / ID: 4ave | ||||||
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Title | C.lacteus nerve Hb in the deoxy form | ||||||
Components | NEURAL HEMOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / NERVE GLOBIN / HEME REACTIVITY / DEOXY STATE / PROTEIN MATRIX TUNNEL | ||||||
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: 1.9 Å | ||||||
Authors | Germani, F. / Pesce, A. / Venturini, A. / Moens, L. / Bolognesi, M. / Dewilde, S. / Nardini, M. | ||||||
Citation | Journal: Int.J.Mol.Sci. / Year: 2012 Title: High Resolution Crystal Structures of the Cerebratulus Lacteus Mini-Hb in the Unligated and Carbomonoxy States. Authors: Germani, F. / Pesce, A. / Venturini, A. / Moens, L. / Bolognesi, M. / Dewilde, S. / Nardini, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ave.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ave.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ave.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4ave ftp://data.pdbj.org/pub/pdb/validation_reports/av/4ave | HTTPS FTP |
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-Related structure data
Related structure data | 4avdC 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: 11546.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CEREBRATULUS LACTEUS (milky ribbon-worm) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O76242 |
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-Non-polymers , 5 types, 126 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: 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: 2.63 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 5.5 Details: 2.6 M AMMONIUM SULFATE, 50 MM SODIUM ACETATE PH 5.5, AT 277 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25.4 Å / Num. obs: 9482 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KR7 Resolution: 1.9→24.99 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.912 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.143 / 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: 15.791 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→24.99 Å
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Refine LS restraints |
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