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Yorodumi- PDB-2fwj: Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fwj | ||||||
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Title | Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) from the acidophilic bacterium Acetobacter aceti, complexed with AIR (5-aminoimidazole ribonucleotide) | ||||||
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: 1.95 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 | 2fwj.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fwj.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fwj_validation.pdf.gz | 823.9 KB | Display | wwPDB validaton report |
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Full document | 2fwj_full_validation.pdf.gz | 826.7 KB | Display | |
Data in XML | 2fwj_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2fwj_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/2fwj ftp://data.pdbj.org/pub/pdb/validation_reports/fw/2fwj | HTTPS FTP |
-Related structure data
Related structure data | 2fw1C 2fw6C 2fw7C 2fw8C 2fw9C 2fwaC 2fwbC 2fwiC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18882.711 Da / Num. of mol.: 2 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: 2.68 Å3/Da / Density % sol: 54.02 % |
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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: Oct 2, 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: 30068 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 17.1 Å2 / Rsym value: 0.064 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2883 / Rsym value: 0.494 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1U11 Resolution: 1.95→35.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 325907.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.9842 Å2 / ksol: 0.356244 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→35.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
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Xplor file |
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