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Yorodumi- PDB-1mgp: Hypothetical protein TM841 from Thermotoga maritima reveals fatty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mgp | ||||||
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Title | Hypothetical protein TM841 from Thermotoga maritima reveals fatty acid binding function | ||||||
Components | Hypothetical protein TM841 | ||||||
Keywords | LIPID BINDING PROTEIN / two domain structure with mixed alpha/beta structures in both domains / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / single anomolous dispersion / Resolution: 2 Å | ||||||
Authors | Schulze-Gahmen, U. / Pelaschier, J. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Proteins / Year: 2003 Title: Crystal structure of a hypothetical protein, TM841 of Thermotoga maritima, reveals its function as fatty acid binding protein Authors: Schulze-Gahmen, U. / Pelaschier, J. / Yokota, H. / Kim, R. / 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 | 1mgp.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mgp.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mgp_validation.pdf.gz | 606.6 KB | Display | wwPDB validaton report |
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Full document | 1mgp_full_validation.pdf.gz | 609.6 KB | Display | |
Data in XML | 1mgp_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1mgp_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/1mgp ftp://data.pdbj.org/pub/pdb/validation_reports/mg/1mgp | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 35937.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pSKB3? / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta/pLysS/Rare / References: UniProt: Q9X1H9 |
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#2: Chemical | ChemComp-PLM / |
#3: 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: 2.42 Å3/Da / Density % sol: 49.24 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: magnesium sulfate, PEG 3350, PEG 400, HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: 5.0.2 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2001 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 45620 / Num. obs: 45541 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.096 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2→2.06 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.357 / % possible all: 99.1 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 417875 / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.4 |
-Processing
Software |
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Refinement | Method to determine structure: single anomolous dispersion / Resolution: 2→19.62 Å / Rfactor Rfree error: 0.004 / 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: 55.1267 Å2 / ksol: 0.438493 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.18 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 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 Å / Lowest resolution: 20 Å / % reflection Rfree: 7.5 % / Rfactor Rfree: 0.2426 / Rfactor Rwork: 0.2204 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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