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Yorodumi- PDB-4aaj: Structure of N-(5'-phosphoribosyl)anthranilate isomerase from Pyr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aaj | ||||||
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Title | Structure of N-(5'-phosphoribosyl)anthranilate isomerase from Pyrococcus furiosus | ||||||
Components | N-(5'-PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE | ||||||
Keywords | ISOMERASE / ALPHA/BETA-BARREL / HYPERTHERMOPHILIC / PHOSPHORIBOSYL ISOMERASE | ||||||
Function / homology | Function and homology information phosphoribosylanthranilate isomerase / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process Similarity search - Function | ||||||
Biological species | PYROCOCCUS FURIOSUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Repo, H. / Oeemig, J.S. / Djupsjobacka, J.B. / Iwai, H. / Heikinheimo, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: A Monomeric Tim-Barrel Structure from Pyrococcus Furiosus is Optimized for Extreme Temperatures Authors: Repo, H. / Oeemig, J.S. / Djupsjobacka, J.B. / Iwai, H. / Heikinheimo, P. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aaj.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aaj.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 4aaj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/4aaj ftp://data.pdbj.org/pub/pdb/validation_reports/aa/4aaj | HTTPS FTP |
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-Related structure data
Related structure data | 1lbmS 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
#1: Protein | Mass: 25196.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PJDJRSF02 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 References: UniProt: Q8U092, phosphoribosylanthranilate isomerase | ||
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#2: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.3 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.5 Details: VAPOR DIFFUSION SITTING DROP, PROTEIN 10MG/ML IN 20 MM MES PH 6.0 MIXED 1:1 WITH 1.8 M AMMONIUM SULPHATE IN 0.1 M SODIUM ACETATE BUFFER, PH 4.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2009 |
Radiation | Monochromator: 2 X CHANNEL-CUT DOUBLE- CRYSTAL SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 22537 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.68 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.85 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LBM Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.916 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.496 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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