+Open data
-Basic information
Entry | Database: PDB / ID: 1nf2 | ||||||
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Title | X-ray crystal structure of TM0651 from Thermotoga maritima | ||||||
Components | phosphatase | ||||||
Keywords | Structural genomics/Unknown function / Thermotoga maritima / Structural proteomics / phosphatase / HAD family / New fold / Structural genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center / Structural genomics-Unknown function COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Shin, D.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima Authors: Shin, D.H. / Roberts, A. / Jancarik, J. / Yokota, H. / Kim, R. / Wemmer, D.E. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nf2.cif.gz | 181.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nf2.ent.gz | 150.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nf2 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nf2 | HTTPS FTP |
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-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: 31227.719 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZB9 #2: Chemical | ChemComp-SO4 / #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: 2.91 Å3/Da / Density % sol: 57.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: AMS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2001 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→83.3 Å / Num. obs: 57785 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.096 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2866 / Rsym value: 0.353 / % possible all: 99.7 |
Reflection | *PLUS Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 99.7 % / Num. unique obs: 2866 / Rmerge(I) obs: 0.353 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→19.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 185871.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.9322 Å2 / ksol: 0.35902 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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