+Open data
-Basic information
Entry | Database: PDB / ID: 3zfi | ||||||
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Title | Rap1a protein (SMA2260) from Serratia marcescens | ||||||
Components | RAP1A PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / BACTERIAL IMMUNITY / 2260 PROTEIN / T6SS / TYPE VI SECRETION SYSTEM / SELF-RESISTANCE PROTEIN | ||||||
Function / homology | 10k-s Protein, Hypothetical Protein A; Chain A - #40 / Rap1a immunity protein / Rap1a immunity proteins / 10k-s Protein, Hypothetical Protein A; Chain A / Orthogonal Bundle / Mainly Alpha / Rap1a protein Function and homology information | ||||||
Biological species | SERRATIA MARCESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Srikannathasan, V. / O'Rourke, P.E.F. / Rao, V.A. / English, G. / Coulthurst, S.J. / Hunter, W.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural Basis for Type Vi Secreted Peptidoglycan Dl-Endopeptidase Function, Specificity and Neutralization in Serratia Marcescens Authors: Srikannathasan, V. / English, G. / Bui, N.K. / Trunk, K. / Rourke, P.E.F.O. / Rao, V.A. / Vollmer, W. / Coulthurst, S.J. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zfi.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zfi.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/3zfi ftp://data.pdbj.org/pub/pdb/validation_reports/zf/3zfi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11827.369 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN (SIGNAL PEPTIDE CLEAVED) Source method: isolated from a genetically manipulated source Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: S4S1V8*PLUS #2: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.53 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 Details: SITTING DROP VAPOUR DIFFUSION. PROTEIN CONCENTRATION AT 9MG/ML, IN 150 MM SODIUM CHLORIDE, 25MM TRIS-HCL, PH 7.5 (SAMPLE BUFFER) RESERVOIR: 25% W/V POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS, ...Details: SITTING DROP VAPOUR DIFFUSION. PROTEIN CONCENTRATION AT 9MG/ML, IN 150 MM SODIUM CHLORIDE, 25MM TRIS-HCL, PH 7.5 (SAMPLE BUFFER) RESERVOIR: 25% W/V POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS, PH 5.5 2:1 SAMPLE TO RESERVOIR RATIO. |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2011 / Details: COMPOUND REFRACTIVE LENSES |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→46.5 Å / Num. obs: 14089 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→61.78 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.28 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: 37.714 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→61.78 Å
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Refine LS restraints |
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