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Yorodumi- PDB-4gyf: Crystal structure of histidinol phosphate phosphatase (HISK) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gyf | |||||||||
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Title | Crystal structure of histidinol phosphate phosphatase (HISK) from Lactococcus lactis subsp. lactis Il1403 complexed with ZN, L-histidinol and phosphate | |||||||||
Components | Histidinol-phosphatase | |||||||||
Keywords | HYDROLASE / PHP fold / histidinol phosphate phosphatase (HISK) / L-histidinol / phosphate | |||||||||
Function / homology | Function and homology information histidinol-phosphatase / histidinol-phosphatase activity / L-histidine biosynthetic process Similarity search - Function | |||||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.647 Å | |||||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Ghodge, S. / Raushel, F.M. / Almo, S.C. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of histidinol phosphate phosphatase (HISK) from Lactococcus lactis subsp. lactis Il1403 complexed with ZN, L-histidinol and phosphate Authors: Fedorov, A.A. / Fedorov, E.V. / Ghodge, S. / Raushel, F.M. / Almo, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gyf.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gyf.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/4gyf ftp://data.pdbj.org/pub/pdb/validation_reports/gy/4gyf | HTTPS FTP |
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-Related structure data
Related structure data | 4gc3S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33235.770 Da / Num. of mol.: 1 / Mutation: R65Q, I127T, K217R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: IL1403 / Gene: hisK, LL1216, L37351 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02150, histidinol-phosphatase |
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-Non-polymers , 7 types, 246 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PO4 / | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.5 M SODIUM CHLORIDE, 0.1M IMIDAZOLE,0.5mM Zinc chloride, 100 mM histidinol phosphate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.647→42.831 Å / Num. all: 40890 / Num. obs: 40890 / % possible obs: 98.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GC3 Resolution: 1.647→42.831 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 16.79 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.647→42.831 Å
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Refine LS restraints |
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LS refinement shell |
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