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Yorodumi- PDB-6xp7: Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xp7 | ||||||
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Title | Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to ADP | ||||||
Components | Nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / Nucleoside diphosphate kinase / phosphotransferase / kinase | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus Af293 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Nguyen, S. / Bruning, J.B. | ||||||
Citation | Journal: Febs J. / Year: 2021 Title: Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase. Authors: Nguyen, S. / Jovcevski, B. / Pukala, T.L. / Bruning, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xp7.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xp7.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xp7_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6xp7_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6xp7_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 6xp7_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/6xp7 ftp://data.pdbj.org/pub/pdb/validation_reports/xp/6xp7 | HTTPS FTP |
-Related structure data
Related structure data | 6xp4SC 6xpsC 6xptC 6xpuC 6xpvC 6xpwC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18056.674 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: ndk1, AFUA_5G03490 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7Z8P9, nucleoside-diphosphate kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.09 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 0.25 M NaCl, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.2→45.782 Å / Num. obs: 23387 / % possible obs: 98.6 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 19.1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 11.1 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XP4 Resolution: 2.2→45.782 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.45 Å2 / Biso mean: 16.5429 Å2 / Biso min: 6.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→45.782 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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