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Yorodumi- PDB-6fcw: Catalytic subunit HisG from Psychrobacter arcticus ATP phosphorib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fcw | ||||||
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Title | Catalytic subunit HisG from Psychrobacter arcticus ATP phosphoribosyltransferase (HisZG ATPPRT) in complex with PRATP | ||||||
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 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 | 6fcw.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fcw.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/6fcw ftp://data.pdbj.org/pub/pdb/validation_reports/fc/6fcw | HTTPS FTP |
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-Related structure data
Related structure data | 6fcaC 6fccC 6fctC 6fcyC 6fd9C 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
#1: Protein | Mass: 25240.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N- and C-termini residues missing from model coordinates due to flexibility - absent from electron density. The first glycine in the sequence 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-PRT / |
#3: Chemical | ChemComp-MG / |
#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: 2.12 Å3/Da / Density % sol: 41.93 % |
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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: 1.5148 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 10, 2017 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5148 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.82 Å / Num. obs: 13619 / % possible obs: 93.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 12.86 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.087 / Rrim(I) all: 0.193 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.621 / Num. unique obs: 915 / CC1/2: 0.72 / Rpim(I) all: 0.325 / Rrim(I) all: 0.704 / % possible all: 88.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Chain E of 5M8H Resolution: 2→23.82 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.714 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.179 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: 52.61 Å2 / Biso mean: 19.516 Å2 / Biso min: 6.61 Å2
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Refinement step | Cycle: final / Resolution: 2→23.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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