+Open data
-Basic information
Entry | Database: PDB / ID: 3i3f | ||||||
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Title | Hypothetical protein from Giardia lamblia GL50803_14299 | ||||||
Components | Hypothetical protein | ||||||
Keywords | UNKNOWN FUNCTION / hypothetical / structural genomics / NIAID / deCODE / infectious disease / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Giardia lamblia (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Hypothetical protein from Giardia lamblia GL50803_14299 Authors: Arakaki, T.L. / Abendroth, J. / Staker, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i3f.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i3f.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 3i3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i3f_validation.pdf.gz | 462 KB | Display | wwPDB validaton report |
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Full document | 3i3f_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 3i3f_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3i3f_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/3i3f ftp://data.pdbj.org/pub/pdb/validation_reports/i3/3i3f | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15567.940 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / Gene: GL50803_14299 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8BD71 #2: Chemical | #3: Chemical | ChemComp-BUA / | #4: Water | ChemComp-HOH / | Nonpolymer details | AUTHOR STATE THA THESE GROUPS WERE MODELED IN RESIDUAL ELECTRON DENSITY BASED UPON THE BEST BIT, ...AUTHOR STATE THA THESE GROUPS WERE MODELED IN RESIDUAL ELECTRON DENSITY BASED UPON THE BEST BIT, BUT THE EXACT IDENTITY OF THE LIGANDS MAY NOT BE CORRECT. | |
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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: 2.17 Å3/Da / Density % sol: 38.87 % |
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Crystal grow | Temperature: 290 K / Method: sitting drop, vapor diffusion / pH: 5.5 Details: 100 mM Tris, pH 5.5, 25% PEG 3350, 200 mM ammonium acetate, sitting drop, vapor diffusion, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC Quantum-315R CCD / Detector: CCD / Date: Jan 1, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→39.41 Å / Num. all: 82643 / Num. obs: 82643 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 13.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→37.35 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.89 / SU B: 0.872 / SU ML: 0.036 / SU R Cruickshank DPI: 0.056 / SU Rfree: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.86 Å2 / Biso mean: 14.501 Å2 / Biso min: 7.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→37.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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