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Yorodumi- PDB-2r85: Crystal structure of PurP from Pyrococcus furiosus complexed with AMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r85 | ||||||
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Title | Crystal structure of PurP from Pyrococcus furiosus complexed with AMP | ||||||
Components | PurP protein PF1517 | ||||||
Keywords | UNKNOWN FUNCTION / ATP-grasp superfamily | ||||||
Function / homology | Function and homology information formate-phosphoribosylaminoimidazolecarboxamide ligase / ligase activity, forming carbon-nitrogen bonds / 'de novo' IMP biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Zhang, Y. / White, R.H. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii. Authors: Zhang, Y. / White, R.H. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r85.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r85.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 2r85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/2r85 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/2r85 | HTTPS FTP |
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-Related structure data
Related structure data | 2r7kSC 2r7lC 2r7mC 2r7nC 2r84C 2r86C 2r87C C: citing same article (ref.) 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | biological assembly is a hexamer or a trimer from the asymmetric unit by the operations: (x,y,z), (-y,x-y,z +(1 1 0)), (-x+y,-x,z) |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38348.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: T7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U0R7 |
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-Non-polymers , 5 types, 664 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-AMP / #5: Chemical | ChemComp-MPD / ( #6: 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: 3.58 Å3/Da / Density % sol: 65.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% MPD, 200 mM NaCl, 100 mM Tris, pH 7.0, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. all: 119607 / Num. obs: 119574 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.052 / Χ2: 0.957 / Net I/σ(I): 12.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2R7K Resolution: 1.7→37.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.446 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.484 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→37.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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