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Yorodumi- PDB-3otn: Crystal structure of a SusD superfamily protein (BDI_3964) from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3otn | ||||||
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Title | Crystal structure of a SusD superfamily protein (BDI_3964) from Parabacteroides distasonis ATCC 8503 at 1.95 A resolution | ||||||
Components | SusD superfamily protein | ||||||
Keywords | SUGAR BINDING PROTEIN / PUTATIVE OUTER MEMBRANE PROTEIN / SUSD / CARBOHYDRATE BINDING / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Parabacteroides distasonis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a SusD superfamily protein (BDI_3964) from Parabacteroides distasonis ATCC 8503 at 1.95 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 | 3otn.cif.gz | 405.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3otn.ent.gz | 334.9 KB | Display | PDB format |
PDBx/mmJSON format | 3otn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3otn_validation.pdf.gz | 480.3 KB | Display | wwPDB validaton report |
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Full document | 3otn_full_validation.pdf.gz | 485.8 KB | Display | |
Data in XML | 3otn_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 3otn_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/3otn ftp://data.pdbj.org/pub/pdb/validation_reports/ot/3otn | 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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2 |
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3 |
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Unit cell |
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Details | SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORTS A MONOMER AS THE SIGNIFICANT OLIGOMERIC STATE IN SOLUTION, WHICH IS CONSISTENT WITH OTHER HOMOLOGS IN THE SAME PROTEIN FAMILY. HOWEVER, CRYSTAL PACKING ANALYSIS SUGGESTS THAT A DIMER MAY ALSO BE A STABLE OLIGOMERIC FORM. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55738.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_3964 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LIX4 |
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-Non-polymers , 5 types, 884 molecules
#2: Chemical | ChemComp-CL / | ||||||
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#3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THIS CONSTRUCT (RESIDUES 26-506) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 26-506) 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: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.17M sodium acetate, 25.3% polyethylene glycol 4000, 15.0% Glycerol, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97918,0.97896 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.95→29.37 Å / Num. all: 76628 / Num. obs: 76628 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.344 Å2 / Rsym value: 0.123 / Net I/σ(I): 7.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.95→29.37 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.999 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.132 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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.CHLORIDE (CL) FROM THE PROTEIN BUFFER; ACETATE (ACT) AND PEG4000 FRAGMENT (PEG) FROM THE CRYSTALLIZATION REAGENT; AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT
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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: 78.7 Å2 / Biso mean: 27.8721 Å2 / Biso min: 10.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 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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