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Yorodumi- PDB-4fuu: Crystal structure of a leucine aminopeptidase precursor (BT_2548)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fuu | ||||||
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Title | Crystal structure of a leucine aminopeptidase precursor (BT_2548) from Bacteroides thetaiotaomicron VPI-5482 at 1.30 A resolution | ||||||
Components | Leucine aminopeptidase | ||||||
Keywords | HYDROLASE / phosphorylase/hydrolase like fold / peptidase family M28 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a leucine aminopeptidase precursor (BT_2548) from Bacteroides thetaiotaomicron VPI-5482 at 1.30 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 | 4fuu.cif.gz | 142.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fuu.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fuu_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 4fuu_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 4fuu_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 4fuu_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/4fuu ftp://data.pdbj.org/pub/pdb/validation_reports/fu/4fuu | 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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Unit cell |
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Details | PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34590.254 Da / Num. of mol.: 1 / Fragment: UNP residues 24-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2548 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A4P9 |
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-Non-polymers , 5 types, 335 molecules
#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#3: Chemical | ChemComp-PO4 / | ||
#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THIS CONSTRUCT (RESIDUES 24-331) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THIS CONSTRUCT (RESIDUES 24-331) 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: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20.00% polyethylene glycol 3350, 0.200M ammonium dihydrogen phosphate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796,0.9793 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011 / Details: KOHZU: Double Crystal Si(111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.3→27.993 Å / Num. all: 64313 / Num. obs: 64313 / % possible obs: 93.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 12.234 Å2 / Rsym value: 0.055 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.3→27.993 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.485 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.045 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. 4.PHOSPHATE (PO4) FROM THE CRYSTALLIZATION BUFFER AND 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 5. THE MODELING OF ZINC IS SUPPORTED BY X-RAY FLUORESCENCE SCANS. THE OCCUPANCY OF THE ZN ATOM WAS REDUCED TO 0.5 FOR ITS REDUCED SCATTERING INDICATED BY ELECTRON DENSITY MAPS. 6. AN UNKNOWN LIGAND (UNL) WAS MODELED AT THE PUTATIVE ACTIVE SITE.
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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: 51.53 Å2 / Biso mean: 17.9771 Å2 / Biso min: 6.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→27.993 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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