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Yorodumi- PDB-2dec: Crystal Structure of the PH0510 protein from Pyrococcus horikoshii OT3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dec | ||||||
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Title | Crystal Structure of the PH0510 protein from Pyrococcus horikoshii OT3 | ||||||
Components | 325aa long hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Mizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the PH0510 protein from Pyrococcus 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 | 2dec.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dec.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dec_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 2dec_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 2dec_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 2dec_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/2dec ftp://data.pdbj.org/pub/pdb/validation_reports/de/2dec | HTTPS FTP |
-Related structure data
Related structure data | 2df8C 2e5fC 1j5xS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 36855.723 Da / Num. of mol.: 2 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: O58246 #2: Chemical | ChemComp-NA / | #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: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.8 Details: PEG 3350, lithium acetate, pH 7.8, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 16, 2005 |
Radiation | Monochromator: Bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 68213 / Num. obs: 68213 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.082 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.81 / Num. unique all: 6735 / Rsym value: 0.301 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J5X Resolution: 1.7→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1503999.75 / 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: 43.4757 Å2 / ksol: 0.3214 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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