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Yorodumi- PDB-3b5q: Crystal structure of a putative sulfatase (NP_810509.1) from Bact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b5q | ||||||
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Title | Crystal structure of a putative sulfatase (NP_810509.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.40 A resolution | ||||||
Components | Putative sulfatase yidJ | ||||||
Keywords | HYDROLASE / NP_810509.1 / Putative Sulfatase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information glucuronate-2-sulfatase activity / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / arylsulfatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative sulfatase (NP_810509.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.40 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b5q.cif.gz | 204.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b5q.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 3b5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/3b5q ftp://data.pdbj.org/pub/pdb/validation_reports/b5/3b5q | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LYS / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 15 - 477 / Label seq-ID: 16 - 478
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THAT THE PROTEIN IS MONOMERIC. THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54342.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Species: Bacteroides thetaiotaomicron / Strain: VPI-5482, DSM 2079, NCTC 10582 / Gene: NP_810509.1, BT_1596 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A7C8 |
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-Non-polymers , 6 types, 398 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE 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: 2.9 Å3/Da / Density % sol: 57.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: NANODROP, 20.0% PEG 8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2007 / Details: Adjustable focusing mirrors in K-B geometry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→29.907 Å / Num. obs: 47977 / % possible obs: 99.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 40.49 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 4.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 2.4→29.907 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.979 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.209 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ZINC HAS BEEN MODELED IN THE STRUCTURE BASED ON AN ANOMALOUS DIFFERENCE FOURIER ELECTRON DENSITY MAP AND COORDINATION GEOMETRY. 4. 1,2-ETHANEDIOL, HEPES AND PARTIAL PEG MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. THERE ARE THREE RAMACHANDRAN OUTLIERS AT POSITIONS A166, B168 AND B297.
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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 mean: 27.428 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.907 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: 5961 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 20
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