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Yorodumi- PDB-4qhx: Crystal structure of a putative two-domain sugar hydrolase (BACCA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qhx | ||||||
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Title | Crystal structure of a putative two-domain sugar hydrolase (BACCAC_02064) from Bacteroides caccae ATCC 43185 at 1.80 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain protein / galactose-binding domain-like fold / concanavalin A-like fold / PF11958 family / DUF3472 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Protein of unknown function DUF3472 / Domain of unknown function DUF5077 / Domain of unknown function (DUF3472) / Domain of unknown function (DUF5077) / DI(HYDROXYETHYL)ETHER / DUF5077 domain-containing protein Function and homology information | ||||||
Biological species | Bacteroides caccae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical protein (BACCAC_02064) from Bacteroides caccae ATCC 43185 at 1.80 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 | 4qhx.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qhx.ent.gz | 149.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/4qhx ftp://data.pdbj.org/pub/pdb/validation_reports/qh/4qhx | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
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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Components on special symmetry positions |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45966.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: BACCAC_02064 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZGP5 |
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-Non-polymers , 5 types, 443 molecules
#2: Chemical | ChemComp-CL / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL 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: 2.68 Å3/Da / Density % sol: 54.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.16M ammonium sulfate, 20.0% Glycerol, 20.0% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, 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: BL14-1 / Wavelength: 0.97934,0.95369,0.97913 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 4, 2014 Details: Vertical focusing mirror; double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→29.643 Å / Num. obs: 43818 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.126 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.27 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.8→29.643 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.846 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.1 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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. 5. GLYCEROL (GOL), SULFATE (SO4), CHLORIDE (CL), AND PEG (PEG) MODELED WERE PRESENT IN CRYSTALLIZATION CONDITIONS.
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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: 83.19 Å2 / Biso mean: 29.4797 Å2 / Biso min: 17.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.643 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 35.6438 Å / Origin y: 7.8641 Å / Origin z: 111.1545 Å
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