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Yorodumi- PDB-3siy: Crystal structure of a DUF1989 family protein (TM1040_0329) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3siy | ||||||
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Title | Crystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040 at 1.35 A resolution | ||||||
Components | DUF1989 family protein | ||||||
Keywords | METAL BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Domain of unknown function DUF1989 / Domain of unknown function (DUF1989) / metal ion binding / DUF1989 domain-containing protein Function and homology information | ||||||
Biological species | Ruegeria sp. TM1040 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040 at 1.35 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 | 3siy.cif.gz | 401.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3siy.ent.gz | 333.8 KB | Display | PDB format |
PDBx/mmJSON format | 3siy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3siy_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 3siy_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | 3siy_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 3siy_validation.cif.gz | 68.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/3siy ftp://data.pdbj.org/pub/pdb/validation_reports/si/3siy | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 26301.660 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruegeria sp. TM1040 (bacteria) / Gene: TM1040_0329 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GJV4 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT 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: 1.95 Å3/Da / Density % sol: 36.83 % Description: INITIAL DATA PROCESSING FOR PHASING WAS DONE WITH XDS AND XSCALE. DUE TO THE PRESENCE OF STRONG ICE RINGS, THE REMOTE WAVELENGTH DATA WERE REPROCESSED FOR REFINEMENT TO EXCLUDE SPOTS ...Description: INITIAL DATA PROCESSING FOR PHASING WAS DONE WITH XDS AND XSCALE. DUE TO THE PRESENCE OF STRONG ICE RINGS, THE REMOTE WAVELENGTH DATA WERE REPROCESSED FOR REFINEMENT TO EXCLUDE SPOTS OVERLAPPING THE ICE RINGS. RESOLUTION BINS 3.91-3.86, 3.70-3.64, 2.26-2.24, 2.08-2.02, 2.30-2.21, 1.96-1.88 AND 1.49-1.46 WERE EXCLUDED FROM INTEGRATION WITH MOSFLM. THE STATISTICS REPORTED IN THE REMARK 200 SECTION ARE FROM THE SCALING OF THE REFINEMENT DATASET WITH SCALA. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 22.0% PEG 3350, 0.1M Magnesium Chloride, 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: 0.91837,0.97971,0.97941 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2010 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.35→58.798 Å / Num. all: 152479 / Num. obs: 152479 / % possible obs: 85.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 10.84 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 1.35→58.798 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 1.796 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.059 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. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF ZINC (ZN) IONS. 4. MAGNESIUM ION (MG) AND CHLORIDE IONS (CL) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. THE DATASET USED FOR REFINEMENT WAS PROCESSED WITH ICE RINGS EXCLUDED FROM INTEGRATION.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.93 Å2 / Biso mean: 15.5987 Å2 / Biso min: 6.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→58.798 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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