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Yorodumi- PDB-3p4g: X-ray crystal structure of a hyperactive, Ca2+-dependent, beta-he... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p4g | ||||||
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Title | X-ray crystal structure of a hyperactive, Ca2+-dependent, beta-helical antifreeze protein from an Antarctic bacterium | ||||||
Components | Antifreeze protein | ||||||
Keywords | ANTIFREEZE PROTEIN / Right-handed Ca2+-binding beta-helix | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Marinomonas primoryensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Garnham, C.P. / Campbell, R.L. / Davies, P.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Anchored clathrate waters bind antifreeze proteins to ice. Authors: Garnham, C.P. / Campbell, R.L. / Davies, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p4g.cif.gz | 490 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p4g.ent.gz | 394.9 KB | Display | PDB format |
PDBx/mmJSON format | 3p4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p4g_validation.pdf.gz | 469.5 KB | Display | wwPDB validaton report |
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Full document | 3p4g_full_validation.pdf.gz | 482.6 KB | Display | |
Data in XML | 3p4g_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 3p4g_validation.cif.gz | 82.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/3p4g ftp://data.pdbj.org/pub/pdb/validation_reports/p4/3p4g | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 33358.715 Da / Num. of mol.: 4 / Fragment: unp residues 997-1318 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Gene: MpAFP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: A1YIY3 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MG / #4: Chemical | #5: 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: 2.51 Å3/Da / Density % sol: 51.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 10% PEG 8000, 400 mM MgAcetate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.6 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34.6 Å / Num. all: 142852 / Num. obs: 135568 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.7 / Num. unique all: 18711 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.06 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.099 / 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: 9.459 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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