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Yorodumi- PDB-3sum: Crystal structure of cerato-platanin 5 from M. perniciosa (MpCP5) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sum | ||||||
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Title | Crystal structure of cerato-platanin 5 from M. perniciosa (MpCP5) | ||||||
Components | Cerato-platanin-like protein | ||||||
Keywords | UNKNOWN FUNCTION / double psi beta barrel | ||||||
Function / homology | Cerato-platanin / Cerato-platanin / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / extracellular region / Mainly Beta / Cerato-platanin-like protein Function and homology information | ||||||
Biological species | Moniliophthora perniciosa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Oliveira, J.F. / Barsottini, M.R.O. / Zaparoli, G. / Machado, L.O. / Dias, S.M.G. / Pereira, G.A.G. / Ambrosio, A.L.B. | ||||||
Citation | Journal: Mol. Plant Microbe Interact. / Year: 2013 Title: Functional diversification of cerato-platanins in Moniliophthora perniciosa as seen by differential expression and protein function specialization. Authors: de O Barsottini, M.R. / de Oliveira, J.F. / Adamoski, D. / Teixeira, P.J. / do Prado, P.F. / Tiezzi, H.O. / Sforca, M.L. / Cassago, A. / Portugal, R.V. / de Oliveira, P.S. / de M Zeri, A.C. ...Authors: de O Barsottini, M.R. / de Oliveira, J.F. / Adamoski, D. / Teixeira, P.J. / do Prado, P.F. / Tiezzi, H.O. / Sforca, M.L. / Cassago, A. / Portugal, R.V. / de Oliveira, P.S. / de M Zeri, A.C. / Dias, S.M. / Pereira, G.A. / Ambrosio, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sum.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sum.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 3sum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/3sum ftp://data.pdbj.org/pub/pdb/validation_reports/su/3sum | HTTPS FTP |
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-Related structure data
Related structure data | 3sujC 3sukC 3sulC 3m3gS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 14944.669 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moniliophthora perniciosa (fungus) / Gene: Cp5 / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI II / References: UniProt: B2C3I4*PLUS #2: Water | ChemComp-HOH / | Sequence details | AS PER THE AUTHORS THE SEQUENCE OF THE CERATO-PLATANIN 5 PROTEIN IS INCORRECT IN THE UNP DATABASE. ...AS PER THE AUTHORS THE SEQUENCE OF THE CERATO-PLATANIN 5 PROTEIN IS INCORRECT IN THE UNP DATABASE. IT IS MISSING THE C-TERMINAL SEQUENCE. | |
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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: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium acetate pH 5.5, 5% PEG 400, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43701 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.43701 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→23.02 Å / Num. all: 51015 / Num. obs: 50913 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.87→1.97 Å / Redundancy: 6 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.327 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3M3G Resolution: 1.87→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.802 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.136 / 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: 21.791 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.917 Å / Total num. of bins used: 20
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