+Open data
-Basic information
Entry | Database: PDB / ID: 4acv | ||||||
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Title | Listeria monocytogenes Antigen B | ||||||
Components | (PROPHAGE LAMBDALM01, ANTIGEN B) x 2 | ||||||
Keywords | IMMUNE SYSTEM / SURFACE / PHAGE-RELATED | ||||||
Function / homology | Domain of unknown function (DUF5072) / STM4215-like - #30 / STM4215-like / 2-Layer Sandwich / Alpha Beta / Prophage LambdaLm01, antigen B / Prophage LambdaLm01, antigen B Function and homology information | ||||||
Biological species | LISTERIA MONOCYTOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.401 Å | ||||||
Authors | Huyet, J. / Naylor, C.E. / Geddes, S. / Basak, A.K. | ||||||
Citation | Journal: To be Published Title: Structure of Listeria Monocytogenes Antigen B Reveals its Relationship to Phage Tail Proteins Authors: Huyet, J. / Naylor, C.E. / Geddes, S. / Basak, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4acv.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4acv.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 4acv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4acv_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 4acv_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 4acv_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 4acv_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/4acv ftp://data.pdbj.org/pub/pdb/validation_reports/ac/4acv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.65004, 0.68173, -0.33569), Vector: |
-Components
#1: Protein | Mass: 14968.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: 10403S / Variant: SEROVAR 1/2A / Plasmid: PET151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G2K1X0, UniProt: A0A0H3G917*PLUS |
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#2: Protein | Mass: 14969.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: 10403S / Variant: SEROVAR 1/2A / Plasmid: PET151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G2K1X0, UniProt: A0A0H3G917*PLUS |
#3: Water | ChemComp-HOH / |
Sequence details | EXPRESSED PROTEIN HAD HIS-TAG WHICH WAS REMOVED. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 4M NA FORMATE, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332, 0.9792 | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 1, 2008 / Details: MIRRORS | |||||||||
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→86.59 Å / Num. obs: 12093 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 30.6 | |||||||||
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 22.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 8.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.401→38.724 Å / SU ML: 0.35 / σ(F): 1.98 / Phase error: 22.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.622 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.401→38.724 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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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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