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Yorodumi- PDB-1x3l: Crystal structure of the PH0495 protein from pyrococccus horikosh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x3l | ||||||
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Title | Crystal structure of the PH0495 protein from pyrococccus horikoshii OT3 | ||||||
Components | hypothetical protein PH0495Hypothesis | ||||||
Keywords | TRANSFERASE / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information glycerate 2-kinase / glycerate 2-kinase activity / glycerate kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the PH0495 protein from pyrococccus horikoshii OT3 Authors: Mizutani, H. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x3l.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x3l.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 1x3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/1x3l ftp://data.pdbj.org/pub/pdb/validation_reports/x3/1x3l | HTTPS FTP |
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-Related structure data
Related structure data | 1o0u S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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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Details | The biological assembly is monomer. |
-Components
#1: Protein | Mass: 47439.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58231, glycerate 3-kinase | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-EDO / #4: 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: 2.81 Å3/Da / Density % sol: 56.23 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.6 Details: ammonium sulfate, acetate, pH 4.6, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 26, 2004 / Details: mirrors |
Radiation | Monochromator: Bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 30781 / Num. obs: 30781 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.01 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.061 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.41 / Num. unique all: 2962 / Rsym value: 0.192 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O0U 1o0u Resolution: 2.1→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1639402.83 / 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: 55.7892 Å2 / ksol: 0.354212 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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