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Yorodumi- PDB-1xqi: Crystal Structure Analysis of an NDP kinase from Pyrobaculum aero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xqi | ||||||
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Title | Crystal Structure Analysis of an NDP kinase from Pyrobaculum aerophilum | ||||||
Components | Nucleoside diphosphate kinaseNucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / alpha/beta sandwich / ferredoxin fold | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrobaculum aerophilum (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Pedelacq, J.D. / Waldo, G.S. / Cabantous, S. / Liong, E.C. / Berendzen, J. / Terwilliger, T.C. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum Authors: Pedelacq, J.D. / Waldo, G.S. / Cabantous, S. / Liong, E.C. / Terwilliger, T.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xqi.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xqi.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/1xqi ftp://data.pdbj.org/pub/pdb/validation_reports/xq/1xqi | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22029.693 Da / Num. of mol.: 3 / Mutation: A10D, G33D, E40K, R71Q, S107N, I117N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: STRAIN IM2 DSM 7523 ATCC 51768 / Gene: ndk / Plasmid: modified pET 28 C-6HIS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZWY4, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | #4: 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: 2.65 Å3/Da / Density % sol: 53.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9792, 0.9791, 0.9500 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2000 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→25 Å / Num. all: 25584 / Num. obs: 22330 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.105 | ||||||||||||
Reflection shell | Resolution: 2.4→2.55 Å / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.26 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.594 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.065 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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