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Yorodumi- PDB-6fd9: Catalytic subunit HisG from Psychrobacter arcticus ATP phosphorib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fd9 | ||||||
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Title | Catalytic subunit HisG from Psychrobacter arcticus ATP phosphoribosyltransferase (HisZG ATPPRT) in complex with AMP | ||||||
Components | ATP phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / phosphoribosyltransferase / HisG / catalytic / cold-adapted | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Psychrobacter arcticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Alphey, M.S. / Ge, Y. / Fisher, G. / Czekster, C.M. / Naismith, J.H. / da Silva, R.G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2018 Title: Catalytic and Anticatalytic Snapshots of a Short-Form ATP Phosphoribosyltransferase Authors: Alphey, M.S. / Fisher, G. / Hirschi, J.S. / Stroek, R. / Ge, Y. / Gould, E.R. / Czekster, C.M. / Liu, H. / Florence, G.J. / Vetticatt, M.J. / Naismith, J.H. / da Silva, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fd9.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fd9.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/6fd9 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/6fd9 | HTTPS FTP |
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-Related structure data
Related structure data | 6fcaC 6fccC 6fctC 6fcwC 6fcyC 6fttC 6fu2C 6fu7C 6fuaC 5m8hS S: Starting model for refinement C: citing same article (ref.) |
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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: 25240.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues from N- and C-termini are missing from coordinate sequence due to flexibility - electron density missing. Initial glycine remains after affinity-tag cleavage. Source: (gene. exp.) Psychrobacter arcticus (strain DSM 17307 / 273-4) (bacteria) Strain: DSM 17307 / 273-4 / Gene: hisG, Psyc_1903 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase |
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#2: Chemical | ChemComp-AMP / |
#3: 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: 2.12 Å3/Da / Density % sol: 42.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: 10mg/ml protein in 20mM Tris HCl pH8.0, 50mM KCl, 10mM MgCl2, 2mM DTT mixed 1:1 with 32% PEG 3350, 0.1M MOPS pH6.5, 0.1M K/Na tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 6, 2017 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→26.61 Å / Num. obs: 10299 / % possible obs: 93 % / Redundancy: 3.6 % / CC1/2: 0.981 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.105 / Rrim(I) all: 0.199 / Net I/σ(I): 5.8 / Num. measured all: 37047 / Scaling rejects: 9 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.549 / Num. unique obs: 827 / CC1/2: 0.706 / Rpim(I) all: 0.336 / Rrim(I) all: 0.645 / % possible all: 87.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M8H chain E Resolution: 2.2→26.61 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.367 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.223 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.29 Å2 / Biso mean: 25.922 Å2 / Biso min: 14.64 Å2
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Refinement step | Cycle: final / Resolution: 2.2→26.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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