+Open data
-Basic information
Entry | Database: PDB / ID: 6vmt | ||||||
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Title | Leishmania major Programmed Cell Death Protein 5 Homolog | ||||||
Components | Programmed Cell Death Protein 5 Homolog | ||||||
Keywords | DNA BINDING PROTEIN / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / DNA binding / nucleus / cytosol / Uncharacterized protein Function and homology information | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å | ||||||
Authors | Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
Citation | Journal: To be published Title: Leishmania major Programmed Cell Death Protein 5 Homolog Authors: Merritt, E.A. / Anderson, L. / Arakaki, T. / Hol, W.G. / Le Trong, I. / Mehlin, C. / Soltis, M. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vmt.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vmt.ent.gz | 21.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vmt_validation.pdf.gz | 248.7 KB | Display | wwPDB validaton report |
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Full document | 6vmt_full_validation.pdf.gz | 248.7 KB | Display | |
Data in XML | 6vmt_validation.xml.gz | 918 B | Display | |
Data in CIF | 6vmt_validation.cif.gz | 1.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/6vmt ftp://data.pdbj.org/pub/pdb/validation_reports/vm/6vmt | HTTPS FTP |
-Related structure data
Related structure data | 6iqoS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13304.014 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_28_1920 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q874 |
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#2: 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: 2.82 Å3/Da / Density % sol: 56.43 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 1.5 M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.95373,0.97962,0.97949 | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2005 | ||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→25.296 Å / Num. obs: 4643 / % possible obs: 87.8 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.04 / Rrim(I) all: 0.122 / Net I/σ(I): 11.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IQO Resolution: 2.501→25.296 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.938 / SU ML: 0.242 / Cross valid method: FREE R-VALUE / ESU R: 0.471 / ESU R Free: 0.306 Details: Hydrogens have been added in their riding positions. Sulfur f'' term set to 2.5e to account for partial substitution of SeMet for Met
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.593 Å2
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Refinement step | Cycle: LAST / Resolution: 2.501→25.296 Å
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Refine LS restraints |
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LS refinement shell |
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