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Yorodumi- PDB-3hze: Crystal Structure of Ycf54 protein from Thermosynechococcus elong... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hze | ||||||
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Title | Crystal Structure of Ycf54 protein from Thermosynechococcus elongatus, Northeast Structural Genomics Consortium Target TeR59 | ||||||
Components | Ycf54 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / TeR59 / Q8DIT2_SYNEL | ||||||
Function / homology | Uncharacterised protein family Ycf54 / Ycf54 protein / Ycf54-like superfamily / Ycf54 protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / PHOSPHATE ION / Ycf54 protein Function and homology information | ||||||
Biological species | Thermosynechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target TeR59 Authors: Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, 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 | 3hze.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hze.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hze_validation.pdf.gz | 478.5 KB | Display | wwPDB validaton report |
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Full document | 3hze_full_validation.pdf.gz | 491.5 KB | Display | |
Data in XML | 3hze_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 3hze_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/3hze ftp://data.pdbj.org/pub/pdb/validation_reports/hz/3hze | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 13674.159 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Strain: BP-1 / Gene: tll1499, ycf54 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8DIT2 #2: Chemical | ChemComp-PO4 / | #3: 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: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.26M NaH2PO4, 0.14M K2HPO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97853 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 133729 / Num. obs: 1028186 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.9 / Num. unique all: 13357 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→20 Å / σ(F): 4209 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 52.944 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.171 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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