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Yorodumi- PDB-3l39: Crystal structure of Putative PhoU-like phosphate regulatory prot... -
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-Basic information
Entry | Database: PDB / ID: 3l39 | ||||||
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Title | Crystal structure of Putative PhoU-like phosphate regulatory protein (BT4638) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.93 A resolution | ||||||
Components | Putative PhoU-like phosphate regulatory protein | ||||||
Keywords | phosphate-binding protein / BT4638 / Putative PhoU-like phosphate regulatory protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Putative phosphate transport regulator / Protein of unknown function DUF47 / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / PHOSPHATE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative PhoU-like phosphate regulatory protein (BT4638) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.93 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l39.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l39.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 3l39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l39_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 3l39_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 3l39_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3l39_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/3l39 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/3l39 | HTTPS FTP |
-Related structure data
Related structure data | 1xwmS 2iiuS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26499.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT4638, BT_4638 / Plasmid: MH4a / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q89YU3 | ||||
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#2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20.0% Glycerol, 1.6M NH4H2PO3, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979245 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2004 / Details: Flat collimating mirror, toroid focusing mirror |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979245 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→44.972 Å / Num. obs: 18980 / % possible obs: 85.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.512 Å2 / Rsym value: 0.071 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2iiu,1xwm Resolution: 1.93→44.972 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.679 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. PHOSPHATES (PO4) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
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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 max: 63.46 Å2 / Biso mean: 14.477 Å2 / Biso min: 3.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→44.972 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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