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Yorodumi- PDB-4gtn: Structure of anthranilate phosphoribosyl transferase from acineto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gtn | ||||||
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Title | Structure of anthranilate phosphoribosyl transferase from acinetobacter baylyi | ||||||
Components | Anthranilate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Phosphoribose binding | ||||||
Function / homology | Function and homology information anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Acinetobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.032 Å | ||||||
Authors | Ponniah, K. / Nigon, L.V. / Anderson, B.F. / Norris, G.E. / Patrick, W.M. | ||||||
Citation | Journal: To be Published Title: Structure of anthranilate phosphoribosyl transferase from acinetobacter baylyi Authors: Ponniah, K. / Nigon, L.V. / Anderson, B.F. / Norris, G.E. / Patrick, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gtn.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gtn.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gtn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gtn_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 4gtn_full_validation.pdf.gz | 432.9 KB | Display | |
Data in XML | 4gtn_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4gtn_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/4gtn ftp://data.pdbj.org/pub/pdb/validation_reports/gt/4gtn | HTTPS FTP |
-Related structure data
Related structure data | 2bpqS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37960.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter (bacteria) / Strain: ADP1 / Gene: trpD / Plasmid: pCA24N-acTrpD / Production host: Escherichia coli (E. coli) / Strain (production host): JMP19 (delta -trpF) References: UniProt: P00500, anthranilate phosphoribosyltransferase |
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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: 2.36 Å3/Da / Density % sol: 47.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.45 Details: 0.1M Na Cacodylate, 15% PEG8000, 0.2M Mg Acetate, pH 7.45, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2008 / Details: Capilliary |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→42.852 Å / Num. obs: 23174 / % possible obs: 98.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1467 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BPQ Resolution: 2.032→42.852 Å / Occupancy max: 1 / Occupancy min: 0.11 / SU ML: 0.23 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.25 Å2 / Biso mean: 39.5524 Å2 / Biso min: 10.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.032→42.852 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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