+Open data
-Basic information
Entry | Database: PDB / ID: 1j9j | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF SURE PROTEIN FROM T.MARITIMA | ||||||
Components | STATIONARY PHASE SURVIVAL PROTEIN | ||||||
Keywords | UNKNOWN FUNCTION / THERMOTOGA MARITIMA / surE protein | ||||||
Function / homology | Function and homology information 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Suh, S.W. / Lee, J.Y. / Kwak, J.E. / Moon, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family. Authors: Lee, J.Y. / Kwak, J.E. / Moon, J. / Eom, S.H. / Liong, E.C. / Pedelacq, J.D. / Berendzen, J. / Suh, S.W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray crystallographic analysis of the surE protein from Thermotoga maritima Authors: Kwak, J.E. / Ha, K.S. / Lee, J.Y. / Im, Y.J. / Park, S.H. / Eom, S.H. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j9j.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j9j.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 1j9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j9j ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j9j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 28107.041 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P96112 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #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: 2.71 Å3/Da / Density % sol: 54.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 296 KDetails: Kwak, J.E., (2001) Acta Crystallogr., Sect.D, 57, 612. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 470499 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.344 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 1.9→36.6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 636611.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.69 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→36.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.245 / % reflection Rfree: 10 % / Rfactor Rwork: 0.199 |