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Yorodumi- PDB-3iv0: Crystal structure of SusD homolog (NP_809186.1) from BACTEROIDES ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iv0 | ||||||
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Title | Crystal structure of SusD homolog (NP_809186.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution | ||||||
Components | SusD homolog | ||||||
Keywords | SUGAR BINDING PROTEIN / NP_809186.1 / SusD homolog / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / RagB / SusD and hypothetical proteins / unknown function | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (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 SusD homolog (NP_809186.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 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 | 3iv0.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iv0.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 3iv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/3iv0 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3iv0 | 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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Unit cell |
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-Components
#1: Protein | Mass: 55631.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_0273, NP_809186.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8AB38 | ||||
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#2: Chemical | ChemComp-CL / | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.12 Å3/Da / Density % sol: 41.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.2000M NaNO3, 20.0000% PEG-3350, No Buffer pH 6.8, 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: 0.91837,0.97848,0.97787 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.35→29.656 Å / Num. obs: 87986 / % possible obs: 86.8 % / Redundancy: 4 % / Biso Wilson estimate: 12.865 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 12.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.35→29.656 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 0.773 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.056 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.CHLORIDE ANION FROM CRYSTALLIZATION AND ETHYLENE GLYCOL FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, RESPECTIVELY. 4.RESIDUE 191 IS CHEMICALLY MODIFIED TO S-HYDROXYCYSTINE WITH ELECTRON DENSITY SUPPORT.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.68 Å2 / Biso mean: 17.65 Å2 / Biso min: 3.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→29.656 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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