+Open data
-Basic information
Entry | Database: PDB / ID: 1wdv | ||||||
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Title | Crystal structure of hypothetical protein APE2540 | ||||||
Components | hypothetical protein APE2540 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / aminoacyl-tRNA editing activity / Alpha-Beta Complex / Alpha Beta / Putative ala-tRNApro hydrolase ProX Function and homology information | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution. Authors: Murayama, K. / Kato-Murayama, M. / Katsura, K. / Uchikubo-Kamo, T. / Yamaguchi-Hirafuji, M. / Kawazoe, M. / Akasaka, R. / Hanawa-Suetsugu, K. / Hori-Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wdv.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wdv.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/1wdv ftp://data.pdbj.org/pub/pdb/validation_reports/wd/1wdv | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16480.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y8U3 #2: 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: 1.93 Å3/Da / Density % sol: 36 % |
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Crystal grow | Temperature: 293 K / pH: 7.6 Details: 16.5% PEG20000, 0.1M HEPES pH 7.6, micro batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.964, 0.9792, 0.9796 | ||||||||||||
Detector | Type: RIGAKU JUPITER / Detector: CCD / Date: Nov 27, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. obs: 31231 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.29 % / Biso Wilson estimate: 13.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 20.9 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 13.5 / Rsym value: 0.12 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→29.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1023667.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.7096 Å2 / ksol: 0.306871 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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