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Yorodumi- PDB-1xm7: The Crystal Structure of the Protein of Unknown Function AQ665 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xm7 | ||||||
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Title | The Crystal Structure of the Protein of Unknown Function AQ665 from Aquifex aeolicus | ||||||
Components | hypothetical protein aq_1665Hypothesis | ||||||
Keywords | Structural genomics / unknown function / protein_aq1665 / protein structure initiative / midwest center for structural genomics / PSI / MCSG | ||||||
Function / homology | Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta / Metallophos_2 domain-containing protein Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Zhang, R. / Zhou, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the hypothetical protein aq_1665 from Aquifex aeolicus Authors: Zhang, R. / Zhou, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xm7.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xm7.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/1xm7 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/1xm7 | 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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1 |
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2 |
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Unit cell |
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Details | This protein existed as monomer.MolA and MolB represent two molecules in the asymmetric unit. |
-Components
#1: Protein | Mass: 23687.150 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O67582 #2: 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: 3.05 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Bis/Tris Propane, 2.8M Sodium Acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.9465 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Oct 26, 2003 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→40 Å / Num. all: 22228 / Num. obs: 21851 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 19.92 | ||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2186 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→29.85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 262072.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs were used in the refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.4573 Å2 / ksol: 0.344659 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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