+Open data
-Basic information
Entry | Database: PDB / ID: 3gbf | ||||||
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Title | Phpd with cadmium complexed with hydroethylphosphonate (HEP) | ||||||
Components | PhpD | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Antibiotic biosynthesis / Iron dependent oxygenase | ||||||
Function / homology | Function and homology information 2-hydroxyethylphosphonate dioxygenase / organic phosphonate biosynthetic process / phosphinothricin biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / antibiotic biosynthetic process / ferrous iron binding / protein homodimerization activity / DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Streptomyces viridochromogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å | ||||||
Authors | Zhang, H. / Nair, S.K. | ||||||
Citation | Journal: To be Published Title: An Unusual Carbon-Carbon Bond Cleavage Reaction in the Biosynthesis of the Herbicide Phosphinothricin Authors: Cicchillio, R.M. / Zhang, H. / Blodgett, J.A.V. / Whitteck, J.T. / Li, G. / Nair, S.K. / van der Donk, W.A. / Metcalf, W.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gbf.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gbf.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gbf_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 3gbf_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 3gbf_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 3gbf_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/3gbf ftp://data.pdbj.org/pub/pdb/validation_reports/gb/3gbf | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48382.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces viridochromogenes (bacteria) Gene: phpD / Plasmid: pET-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5IW40 | ||
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#2: Chemical | ChemComp-2HE / ( | ||
#3: Chemical | ChemComp-CD / #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: 2.11 Å3/Da / Density % sol: 41.76 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 M sodium acetate, 100 mM Hepes pH 7.5, 50 mM Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 31537 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.069 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 2916 / Rsym value: 0.29 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.92→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.168 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 26.621 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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