+Open data
-Basic information
Entry | Database: PDB / ID: 2nsh | ||||||
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Title | E. coli PurE H45Q mutant complexed with nitro-AIR | ||||||
Components | Phosphoribosylaminoimidazole carboxylase catalytic subunit | ||||||
Keywords | LYASE / central three-layer alpha-beta-alpha sandwich / kinked C-terminal helix | ||||||
Function / homology | Function and homology information 5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ealick, S.E. / Morar, M. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: N(5)-CAIR Mutase: Role of a CO(2) Binding Site and Substrate Movement in Catalysis. Authors: Hoskins, A.A. / Morar, M. / Kappock, T.J. / Mathews, I.I. / Zaugg, J.B. / Barder, T.E. / Peng, P. / Okamoto, A. / Ealick, S.E. / Stubbe, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nsh.cif.gz | 47.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nsh.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 2nsh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/2nsh ftp://data.pdbj.org/pub/pdb/validation_reports/ns/2nsh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17789.252 Da / Num. of mol.: 1 / Mutation: H45Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: purE / Production host: Escherichia coli (E. coli) References: UniProt: P0AG18, phosphoribosylaminoimidazole carboxylase |
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#2: Chemical | ChemComp-NIA / (( |
#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: 2.16 Å3/Da / Density % sol: 43.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG400, 0.2M magnesium chloride, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39.5 Å / Num. all: 14561 / Num. obs: 12061 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.91 Å / % possible all: 77.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.886 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.136 / 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: 38.332 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→39.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.0094 Å / Origin y: -24.7703 Å / Origin z: -15.9583 Å
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