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Yorodumi- PDB-4ef2: Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ef2 | ||||||
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Title | Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 2.10 A resolution | ||||||
Components | Pheromone cOB1/lipoprotein, YaeC family | ||||||
Keywords | METHIONINE-BINDING PROTEIN / periplasmic methionine binding protein / NLPA lipoprotein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 2.10 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 | 4ef2.cif.gz | 202.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ef2.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ef2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/4ef2 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/4ef2 | 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27470.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_2496 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q831K8 |
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-Non-polymers , 6 types, 105 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-PGE / | #5: Chemical | #6: Chemical | ChemComp-PE8 / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THIS CONSTRUCT (RESIDUES 28-272) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 28-272) 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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 30.0% polyethylene glycol 400, 0.1M CHES pH 9.5, 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: BL11-1 / Wavelength: 0.91837,0.97966,0.97901 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→28.763 Å / Num. obs: 28845 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.876 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.1→28.763 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.455 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.191 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 RECORD CONTAINS 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.PEG FRAGMENTS (PEG, PGE AND PE8) FROM THE CRYSTALLIZATION SOLUTION AND CHLORIDE (CL) FROM THE PURIFICATION BUFFER HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.SELENO-METHIONINE (MSE) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON PUTATIVE ASSIGNMENT OF FUNCTION FROM PROTEIN STRUCTURE COMPARISONS AND ANOMALOUS DIFFERENCE FOURIER ELECTRON DENSITY MAPS. 7.RAMACHANDRAN OUTLIERS AT PHE84 IN BOTH PROTEIN ARE SUPPORTED BY ELECTRON DENSITY AND LIE IN THE VICINITY OF THE PUTATIVE ACTIVE SITE. 8.NCS RESTRAINTS WERE APPLIED USING REFMAC's LOCAL NCS OPTION (NCSR LOCAL). NCS GROUP 1 CHAIN A (30-270 TO CHAIN B (30-270) COUNT: 8183, RMS: 0.12, WEIGHT: 0.05.
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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: 121.37 Å2 / Biso mean: 52.5789 Å2 / Biso min: 23.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→28.763 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.102→2.156 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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