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Yorodumi- PDB-2fwi: Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fwi | ||||||
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Title | Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) H59D, from the acidophilic bacterium Acetobacter aceti, complexed with 5-aminoimidazole ribonucleotide (AIR) | ||||||
Components | N5-carboxyaminoimidazole ribonucleotide mutase | ||||||
Keywords | LYASE / acidophile / PurE / purine biosynthesis | ||||||
Function / homology | Function and homology information 5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process Similarity search - Function | ||||||
Biological species | Acetobacter aceti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.94 Å | ||||||
Authors | Starks, C.M. / Kappock, T.J. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Biochemical and Structural Studies of N(5)-Carboxyaminoimidazole Ribonucleotide Mutase from the Acidophilic Bacterium Acetobacter aceti. Authors: Constantine, C.Z. / Starks, C.M. / Mill, C.P. / Ransome, A.E. / Karpowicz, S.J. / Francois, J.A. / Goodman, R.A. / Kappock, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fwi.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fwi.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/2fwi ftp://data.pdbj.org/pub/pdb/validation_reports/fw/2fwi | HTTPS FTP |
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-Related structure data
Related structure data | 2fw1C 2fw6C 2fw7C 2fw8C 2fw9C 2fwaC 2fwbC 2fwjC 2fwpC 1u11S 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: 18859.650 Da / Num. of mol.: 2 / Mutation: H59D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetobacter aceti (bacteria) / Strain: 1023 / Gene: purE / Plasmid: pET-23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / References: UniProt: Q2QJL3 #2: Chemical | ChemComp-AIR / | #3: 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: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M lithium sulfate, 0.1M Tris pH 8, 30% (w/v) PEG 4000 (soaked at pH 7), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 111 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 9, 2005 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 30234 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.066 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2969 / Rsym value: 0.518 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1U11 Resolution: 1.94→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.508 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.118 / 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: 23.367 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.943→1.993 Å / Total num. of bins used: 20
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