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Yorodumi- PDB-4lt9: Crystal Structure of Engineered Protein, Northeast Structural Gen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lt9 | ||||||
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Title | Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR404 | ||||||
Components | Engineered Protein OR404 | ||||||
Keywords | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Engineered Protein | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Function and homology information | ||||||
Biological species | artificial gene (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Sahdev, S. / Xiao, R. / Kogan, S. / Maglaqui, M. / Baker, D. ...Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Sahdev, S. / Xiao, R. / Kogan, S. / Maglaqui, M. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Engineered Protein OR404. Authors: Vorobiev, S. / Su, M. / Bjelic, S. / Kipnis, Y. / Wang, L. / Sahdev, S. / Xiao, R. / Kogan, S. / Maglaqui, M. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lt9.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lt9.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 4lt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lt9_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 4lt9_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 4lt9_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4lt9_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/4lt9 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/4lt9 | HTTPS FTP |
-Related structure data
Related structure data | 4a2rS 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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Details | monomer,30.47 kD,95.4% |
-Components
#1: Protein | Mass: 31082.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) / Plasmid: OR404-29.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic |
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#2: 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: 1.87 Å3/Da / Density % sol: 34.26 % |
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Crystal grow | Temperature: 277 K / Method: microbatch crystallization under oil / pH: 8 Details: 24% PEG 20000, 0.1M potassium chloride, 0.1M TrisHCl, pH 8.0, Microbatch crystallization under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 24563 / Num. obs: 24498 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 37.77 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.01176 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3130 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 4A2R Resolution: 2.15→36.667 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.109 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.24 Å2 / Biso mean: 51.422 Å2 / Biso min: 12.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→36.667 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 7.8619 Å / Origin y: 37.6065 Å / Origin z: 49.6147 Å
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Refinement TLS group | Selection details: chain A |