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Yorodumi- PDB-3m1x: Crystal structure of a putative endoribonuclease L-PSP from Entam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m1x | ||||||
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Title | Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica, rhomobohedral form | ||||||
Components | putative Endoribonuclease L-PSP | ||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica, rhomobohedral form Authors: Gardberg, A. / Abendroth, J. / Davies, D. / Staker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m1x.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m1x.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 3m1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m1x_validation.pdf.gz | 446.4 KB | Display | wwPDB validaton report |
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Full document | 3m1x_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 3m1x_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 3m1x_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/3m1x ftp://data.pdbj.org/pub/pdb/validation_reports/m1/3m1x | HTTPS FTP |
-Related structure data
Related structure data | 1xrgS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15656.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI_087570 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4LXT9 |
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#2: Chemical | ChemComp-FLC / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-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: 27.25 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: INDEX SCREEN CONDITION D4: 100MM CITRATE, 25% PEG 3350, ENHIA.00579.A AT 25.8 MG/ML, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979464 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979464 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→54.09 Å / Num. all: 32783 / Num. obs: 32477 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.047 |
Reflection shell | Resolution: 1.2→1.27 Å / Redundancy: 5 % / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XRG modified with CCP4 program CHAINSAW Resolution: 1.2→54.085 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.812 / SU ML: 0.017 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 8.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→54.085 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.24 Å / Total num. of bins used: 20
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