+Open data
-Basic information
Entry | Database: PDB / ID: 1b9a | ||||||
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Title | PARVALBUMIN (MUTATION;D51A, F102W) | ||||||
Components | PROTEIN (PARVALBUMIN) | ||||||
Keywords | CALCIUM BINDING PROTEIN / EF-HAND PROTEINS / PARVALBUMIN / CALCIUM-BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cyprinus carpio (common carp) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Cates, M.S. / Berry, M.B. / Ho, E.L. / Li, Q. / Potter, J.D. / Phillips Jr., G.N. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Metal-ion affinity and specificity in EF-hand proteins: coordination geometry and domain plasticity in parvalbumin. Authors: Cates, M.S. / Berry, M.B. / Ho, E.L. / Li, Q. / Potter, J.D. / Phillips Jr., G.N. #1: Journal: J.Biol.Chem. / Year: 1989 Title: Restrained Least Squares Refinement of Native (Calcium) and Cadmium- Substituted Carp Parvalbumin Using X-Ray Crystallographic Data at 1.6 Angstrom Resolution Authors: Swain, A.L. / Kretsinger, R.H. / Amma, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b9a.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b9a.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1b9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b9a_validation.pdf.gz | 409.7 KB | Display | wwPDB validaton report |
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Full document | 1b9a_full_validation.pdf.gz | 411.4 KB | Display | |
Data in XML | 1b9a_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1b9a_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/1b9a ftp://data.pdbj.org/pub/pdb/validation_reports/b9/1b9a | HTTPS FTP |
-Related structure data
Related structure data | 1b8cC 1b8lC 1b8rC 5cpvS 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: 11445.816 Da / Num. of mol.: 1 / Mutation: D51A, F102W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyprinus carpio (common carp) / Production host: Escherichia coli (E. coli) / References: UniProt: P02618 | ||
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#2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 41.44 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.743318 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.743318 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 5432 / % possible obs: 73 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.069 |
Reflection | *PLUS % possible obs: 73 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CPV, AUTH A.L.SWAIN,R.H.KRETSINGER, E.L.AMMA Resolution: 2→40 Å / Rfactor Rfree error: 0.012 / Data cutoff high rms absF: 723489.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.41 Å2 / ksol: 0.3181 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.2096 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.403 / % reflection Rfree: 12.2 % / Rfactor Rwork: 0.275 |