+Open data
-Basic information
Entry | Database: PDB / ID: 1rwy | ||||||
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Title | CRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN AT 1.05 RESOLUTION | ||||||
Components | PARVALBUMIN ALPHA | ||||||
Keywords | CALCIUM-BINDING PROTEIN / EF-HAND / CALCIUM-BINDING | ||||||
Function / homology | Function and homology information inhibitory chemical synaptic transmission / cuticular plate / excitatory chemical synaptic transmission / stereocilium / cochlea development / terminal bouton / gene expression / axon / neuronal cell body / calcium ion binding ...inhibitory chemical synaptic transmission / cuticular plate / excitatory chemical synaptic transmission / stereocilium / cochlea development / terminal bouton / gene expression / axon / neuronal cell body / calcium ion binding / protein-containing complex binding / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Bottoms, C.A. / Schuermann, J.P. / Agah, S. / Henzl, M.T. / Tanner, J.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Crystal Structure of Rat Alpha-Parvalbumin at 1.05 Resolution Authors: Bottoms, C.A. / Schuermann, J.P. / Agah, S. / Henzl, M.T. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rwy.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rwy.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rwy_validation.pdf.gz | 470.2 KB | Display | wwPDB validaton report |
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Full document | 1rwy_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | 1rwy_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1rwy_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/1rwy ftp://data.pdbj.org/pub/pdb/validation_reports/rw/1rwy | HTTPS FTP |
-Related structure data
Related structure data | 1rtpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 11813.341 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: FAST-TWITCH MUSCLE / Gene: PVALB, PVA / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P02625 |
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-Non-polymers , 6 types, 386 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACY / | #5: Chemical | ChemComp-NH4 / | #6: Chemical | ChemComp-PG4 / | #7: Water | ChemComp-HOH / | |
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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: 1.69 Å3/Da / Density % sol: 27.1 % Description: CNS WAS USED TO REFINE THE STARTING MODEL WITH A 1.55 DATA. SET WAS COLLECTED AT HOME. SHELX WAS USED TO REFINE THE RESULTING MODEL WITH THE 1.05 A DATASET COLLECTED AT APS-ID. |
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Crystal grow | Temperature: 298 K / pH: 4.6 Details: PEG, ammonium sulfate, sodium acetate, temperature 298K, pH 4.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.94644 |
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 17, 2003 / Details: APS 19-ID |
Radiation | Monochromator: APS 19-ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94644 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→25.1 Å / Num. obs: 132869 / % possible obs: 99.2 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.6 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RTP Resolution: 1.05→25.1 Å / Num. parameters: 26422 / Num. restraintsaints: 31383 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.024
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Solvent computation | Solvent model: SWAT (BABINET'S PRINCIPLE) (MOEWS & KRETSINGER). | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 2371 / Occupancy sum non hydrogen: 2867.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→25.1 Å
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Refine LS restraints |
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