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Yorodumi- PDB-3gxh: Crystal structure of Putative phosphatase (DUF442) (YP_001181608.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gxh | ||||||
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Title | Crystal structure of Putative phosphatase (DUF442) (YP_001181608.1) from SHEWANELLA PUTREFACIENS CN-32 at 1.40 A resolution | ||||||
Components | Putative phosphatase (DUF442) | ||||||
Keywords | HYDROLASE / YP_001181608.1 / Putative phosphatase (DUF442) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / tyrosine phosphatase | ||||||
Function / homology | Beta-lactamase hydrolase-like protein, phosphatase-like domain / Beta-lactamase hydrolase-like protein, phosphatase-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase-like / hydrolase activity / Alpha-Beta Complex / Alpha Beta / Beta-lactamase hydrolase-like protein phosphatase-like domain-containing protein Function and homology information | ||||||
Biological species | Shewanella putrefaciens CN-32 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative phosphatase (DUF442) (YP_001181608.1) from SHEWANELLA PUTREFACIENS CN-32 at 1.40 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gxh.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gxh.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 3gxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gxh ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gxh | 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY INDICATES THAT THE MONOMERIC FORM IS A SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 17797.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria) Gene: Sputcn32_0073, YP_001181608.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A4Y1H6 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 23-178) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 23-178) WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.14 Å3/Da / Density % sol: 42.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.0000M (NH4)2SO4, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97828 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 18, 2009 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97828 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→48.853 Å / Num. obs: 60504 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 15.951 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.65 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→48.853 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.061 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.058 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.85 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. CL, SO4, EDO MODELED IS PRESENT IN CRYTALLIZATION OR CRYO SOLUTION.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.35 Å2 / Biso mean: 18.26 Å2 / Biso min: 7.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→48.853 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1774 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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