+Open data
-Basic information
Entry | Database: PDB / ID: 2vq8 | ||||||
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Title | RNASE ZF-1A | ||||||
Components | RNASE ZF-1A | ||||||
Keywords | HYDROLASE / EVOLUTION / ZEBRAFISH / POLYMORPHISM / RIBONUCLEASES | ||||||
Function / homology | P-30 Protein / Ribonuclease A-like domain / Roll / Alpha Beta Function and homology information | ||||||
Biological species | DANIO RERIO (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Kazakou, K. / Holloway, D.E. / Prior, S.H. / Subramanian, V. / Acharya, K.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Ribonuclease A Homologues of the Zebrafish: Polymorphism, Crystal Structures of Two Representatives and Their Evolutionary Implications. Authors: Kazakou, K. / Holloway, D.E. / Prior, S.H. / Subramanian, V. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vq8.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vq8.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vq8_validation.pdf.gz | 424 KB | Display | wwPDB validaton report |
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Full document | 2vq8_full_validation.pdf.gz | 424.2 KB | Display | |
Data in XML | 2vq8_validation.xml.gz | 9 KB | Display | |
Data in CIF | 2vq8_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vq8 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vq8 | HTTPS FTP |
-Related structure data
Related structure data | 2vq9C 1angS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 15899.014 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: PYSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST 11 RESIDUES MET(-11) TO MET(-1), INCLUDING THE OBSERVED RESIDUES HIS(-2) AND MET(-1), ARE ...THE FIRST 11 RESIDUES MET(-11) TO MET(-1), INCLUDING THE OBSERVED RESIDUES HIS(-2) AND MET(-1), ARE PART OF THE HIS-TAG |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE |
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Crystal grow | pH: 8 Details: 25% PEG 4000, 0.2M AMMONIUM SULPHATE, 0.1M TRIS-HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 18, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 27012 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2 / % possible all: 61.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ANG Resolution: 1.35→23.24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.038 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.071 / 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: 11.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→23.24 Å
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Refine LS restraints |
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