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Yorodumi- PDB-1k26: Structure of a Nudix Protein from Pyrobaculum aerophilum Solved b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k26 | ||||||
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Title | Structure of a Nudix Protein from Pyrobaculum aerophilum Solved by the Single Wavelength Anomolous Scattering Method | ||||||
Components | NUDIX HOMOLOG | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NUDIX/MUTT-LIKE FOLD / MIXED ALPHA/BETA / DIMER / PUTATIVE NUDIX HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrobaculum aerophilum (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Wang, S. / Mura, C. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets. Authors: Wang, S. / Mura, C. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k26.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k26.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 1k26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/1k26 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/1k26 | 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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Details | The biological assembly is a dimer as in the asymmetric unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17813.570 Da / Num. of mol.: 2 / Mutation: M16L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Plasmid: PET-22B_MUTT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZTD8 |
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-Non-polymers , 6 types, 165 molecules
#2: Chemical | #3: Chemical | ChemComp-IR3 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACY / #7: 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: 2.26 Å3/Da / Density % sol: 45.57 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: PEG 4000, ammonium sulfate, sodium acetate, isopropanol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1053 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1053 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100 Å / Num. all: 25455 / Num. obs: 25455 / % possible obs: 89.3 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.076 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.25 % / Mean I/σ(I) obs: 3.15 / Num. unique all: 1452 / Rsym value: 0.47 / % possible all: 52 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 348337 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 52 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→19.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 150296.42 / 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: 61.2892 Å2 / ksol: 0.445339 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→19.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.182 / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.287 / Rfactor Rwork: 0.246 |