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Yorodumi- PDB-6fua: ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fua | ||||||
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Title | ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus in complex with PRPP and ADP | ||||||
Components |
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Keywords | TRANSFERASE / ATP phosphoribosyltransferase / HisZG / cold-adapted | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Psychrobacter arcticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 | 6fua.cif.gz | 238 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fua.ent.gz | 187.1 KB | Display | PDB format |
PDBx/mmJSON format | 6fua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/6fua ftp://data.pdbj.org/pub/pdb/validation_reports/fu/6fua | HTTPS FTP |
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-Related structure data
Related structure data | 6fcaC 6fccC 6fctC 6fcwC 6fcyC 6fd9C 6fttC 6fu2C 6fu7C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 43129.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Missing sections are due to flexible regions not visible in the electron density maps. N-terminal Gly remains after tag cleavage. Source: (gene. exp.) Psychrobacter arcticus (strain DSM 17307 / 273-4) (bacteria) Strain: DSM 17307 / 273-4 / Gene: hisZ, Psyc_0676 / Plasmid: pJexpress414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4FTX3 #2: Protein | Mass: 25240.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Missing sections are due to flexible regions not visible in the electron density maps. N-terminal Gly remains after tag cleavage. Source: (gene. exp.) Psychrobacter arcticus (strain DSM 17307 / 273-4) (bacteria) Strain: DSM 17307 / 273-4 / Gene: hisG, Psyc_1903 / Plasmid: pJexpress431 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43(DE3) / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase |
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-Sugars , 1 types, 2 molecules
#5: Sugar |
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-Non-polymers , 4 types, 27 molecules
#3: Chemical | #4: Chemical | #6: Chemical | ChemComp-MG / | #7: 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: 2.48 Å3/Da / Density % sol: 50.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8mg mL-1 protein (in 20mM Tris pH7, 50mM KCl, 10mM MgCl2, 2mM DTT, 0.5mM histidine) mixed in 1:1 ratio with precipitant solution (11% PEG3350, 100mM bicine pH8.5, 150mM SrCl2, 150mM KBr, 2% 1,6-hexanediol) |
-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: Mar 3, 2017 / Details: Varimax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→35.04 Å / Num. obs: 32533 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.115 / Rrim(I) all: 0.224 / Net I/σ(I): 6.4 / Num. measured all: 120442 / Scaling rejects: 46 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.707 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4710 / CC1/2: 0.581 / Rpim(I) all: 1.032 / Rrim(I) all: 1.998 / % possible all: 98.6 |
-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 partial model Resolution: 2.8→35.04 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.876 / SU B: 26.197 / SU ML: 0.445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439 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: 138.05 Å2 / Biso mean: 65.218 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 2.8→35.04 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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