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- PDB-2fw6: Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fw6 | ||||||
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Title | Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) mutant H59N from the acidophilic bacterium Acetobacter aceti, at pH 5.4 | ||||||
![]() | N5-carboxyaminoimidazole ribonucleotide mutase | ||||||
![]() | LYASE / acidophile / PurE / purine biosynthesis | ||||||
Function / homology | ![]() 5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Starks, C.M. / Kappock, T.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 58.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.8 KB | Display | ![]() |
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Full document | ![]() | 456.4 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fw1C ![]() 2fw7C ![]() 2fw8C ![]() 2fw9C ![]() 2fwaC ![]() 2fwbC ![]() 2fwiC ![]() 2fwjC ![]() 2fwpC ![]() 1u11S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18858.666 Da / Num. of mol.: 2 / Mutation: H59N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CIT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 21% (w/v) PEG 4000 190 mM ammonium acetate 90 mM sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 111 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 27, 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: 1.85→50 Å / Num. obs: 33762 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.055 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2779 / Rsym value: 0.389 / % possible all: 80.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1u11 Resolution: 1.85→42.35 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 389806.79 / 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: 50.2034 Å2 / ksol: 0.357859 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→42.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.92 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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Xplor file |
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