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Yorodumi- PDB-3i7a: Crystal structure of Putative metal-dependent phosphohydrolase (Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i7a | ||||||
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Title | Crystal structure of Putative metal-dependent phosphohydrolase (YP_926882.1) from Shewanella amazonensis SB2B at 2.06 A resolution | ||||||
Components | Putative metal-dependent phosphohydrolase | ||||||
Keywords | HYDROLASE / YP_926882.1 / Putative metal-dependent phosphohydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Metal-dependent hydrolase HDOD / HDOD domain / HD-related output (HDOD) domain profile. / Hypothetical protein af1432 / Hypothetical protein af1432 / Orthogonal Bundle / Mainly Alpha / Putative signal transduction protein Function and homology information | ||||||
Biological species | Shewanella amazonensis SB2B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.06 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative metal-dependent phosphohydrolase (YP_926882.1) from Shewanella amazonensis SB2B at 2.06 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 | 3i7a.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i7a.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 3i7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i7a_validation.pdf.gz | 412.2 KB | Display | wwPDB validaton report |
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Full document | 3i7a_full_validation.pdf.gz | 413.4 KB | Display | |
Data in XML | 3i7a_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3i7a_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/3i7a ftp://data.pdbj.org/pub/pdb/validation_reports/i7/3i7a | 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: 31366.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella amazonensis SB2B (bacteria) / Gene: Sama_1005, YP_926882.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S4A6 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE CONSTRUCT (RESIDUES 1-280) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-280) WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND . Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 | Details: 20.0000% PEG-6000, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97839,0.97799 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.06→29.476 Å / Num. obs: 20761 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.504 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.62 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.06→29.476 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.235 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.171 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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
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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: 72.72 Å2 / Biso mean: 26.543 Å2 / Biso min: 8.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→29.476 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.115 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.6305 Å / Origin y: 28.8356 Å / Origin z: 29.1566 Å
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