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Yorodumi- PDB-4ntl: Crystal structure of a lipoprotein, YaeC family (EF3198) from Ent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ntl | ||||||
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Title | Crystal structure of a lipoprotein, YaeC family (EF3198) from Enterococcus faecalis V583 at 1.80 A resolution | ||||||
Components | Lipoprotein, YaeC family | ||||||
Keywords | TRANSPORT PROTEIN / NLPA lipoprotein / PF03180 family / 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: 1.799 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a lipoprotein, YaeC family (EF3198) from Enterococcus faecalis V583 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 | 4ntl.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ntl.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ntl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ntl_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 4ntl_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 4ntl_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4ntl_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/4ntl ftp://data.pdbj.org/pub/pdb/validation_reports/nt/4ntl | 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27676.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: EF_3198, I574_00285, NP_816800.1, OO5_00380 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q82Z74 |
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-Non-polymers , 5 types, 291 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THIS CONSTRUCT (RESIDUES 27-272) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 27-272) 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: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6 Details: 0.2000M zinc acetate, 10.0000% polyethylene glycol 8000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979347,0.918401,0.979261 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC Q315 / Detector: CCD / Date: Oct 17, 2013 / 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: 1.799→29.013 Å / Num. all: 32421 / Num. obs: 32421 / % possible obs: 100 % / Redundancy: 13.8 % / Rsym value: 0.168 / Net I/σ(I): 11.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.019 / 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: 1.799→29.013 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 4.326 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.WATERS WERE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS 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. ZINC (ZN) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO THE STRUCTURE. THE MODELING OF ZINC IS SUPPORTED BY ANOMALOUS DIFFERENCE ELECTRON DENSITY MAPS.6. 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 7.SODIUM (NA) FROM THE PURIFICATION BUFFER AND ACETATE (ACT) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE.
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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: 115.29 Å2 / Biso mean: 29.1971 Å2 / Biso min: 11.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.799→29.013 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.845 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 5.2479 Å / Origin y: 34.2901 Å / Origin z: 19.3299 Å
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