+Open data
-Basic information
Entry | Database: PDB / ID: 4m4c | ||||||
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Title | Crystal structure of Rhodostomin ARGDP mutant | ||||||
Components | Zinc metalloproteinase/disintegrin | ||||||
Keywords | TOXIN / Rhodostomin / disintegrin / integrin / ARGDP / Loss-of-function | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Calloselasma rhodostoma (Malayan pit viper) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chang, Y.T. / Jeng, W.Y. / Shiu, J.H. / Chen, C.Y. / Chuang, W.J. | ||||||
Citation | Journal: To be Published Title: Effect of C-terminal proline residue adjacent to the RGD motif in rhodostomin on its activity and structure Authors: Chang, Y.T. / Jeng, W.Y. / Shiu, J.H. / Chen, C.Y. / Chuang, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m4c.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m4c.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 4m4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/4m4c ftp://data.pdbj.org/pub/pdb/validation_reports/m4/4m4c | HTTPS FTP |
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-Related structure data
Related structure data | 3uciS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 4 - 40 / Label seq-ID: 4 - 40
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-Components
#1: Protein | Mass: 7281.243 Da / Num. of mol.: 4 / Fragment: UNP residues 408-475 / Mutation: P48A, M52P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper) Gene: RHOD / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 References: UniProt: P30403, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Chemical | ChemComp-SO4 / #3: 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: 1.96 Å3/Da / Density % sol: 37.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG4000, 0.2M Ammonium sulfate, 5% PEG3350, 2% PEG200, 0.5% 2-propanol(External) , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 2, 2013 Details: Vertically Focusing Mirror, Horizontally Focusing Single Crystal Si(111) Bent Monochromator |
Radiation | Monochromator: Horizontally Focusing Single Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 20296 / Num. obs: 19633 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.3 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UCI Resolution: 1.8→23.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.14 / SU ML: 0.126 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.843 / ESU R Free: 0.146 / 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: 33.953 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→23.58 Å
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Refine LS restraints |
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