+Open data
-Basic information
Entry | Database: PDB / ID: 2fsu | ||||||
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Title | Crystal Structure of the PhnH Protein from Escherichia Coli | ||||||
Components | Protein phnH | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / C-P Lyase / PhnH / phosphonate metabolism / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | Function and homology information alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity / alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex / carbon phosphorus lyase complex / organic phosphonate metabolic process / organic phosphonate transport / organic phosphonate catabolic process / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Adams, M.A. / Luo, Y. / Zechel, D.L. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: J.Bacteriol. / Year: 2008 Title: Crystal structure of PhnH: an essential component of carbon-phosphorus lyase in Escherichia coli. Authors: Adams, M.A. / Luo, Y. / Hove-Jensen, B. / He, S.M. / van Staalduinen, L.M. / Zechel, D.L. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fsu.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fsu.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 2fsu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fsu_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 2fsu_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 2fsu_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 2fsu_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/2fsu ftp://data.pdbj.org/pub/pdb/validation_reports/fs/2fsu | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 23111.387 Da / Num. of mol.: 1 / Fragment: PhnH / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P16686 | ||||
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#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-ACT / | #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: 1.93 Å3/Da / Density % sol: 36.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: magnesium acetate, PEG 4000, sodium citrate pH 3.5 with protein in HEPES buffer, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979029, 0.978681, 0.925256 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2005 | ||||||||||||
Radiation | Monochromator: Monochromator: Si(111) channel cut monochromator. Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.57→50 Å / Num. all: 24912 / Num. obs: 24912 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.045 / Net I/σ(I): 42 | ||||||||||||
Reflection shell | Resolution: 1.57→1.77 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / % possible all: 35.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→38.92 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.994 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.127 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.678 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→38.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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